Cyclus Archetypes

Cyclus Archetypes

Anthony M. Scopatz Matthew J. Gidden Robert W. Carlsen Robert R. Flanagan Kathryn D. Huff Meghan B. McGarry Arrielle C. Opotowsky Olzhas Rakhimov Zach Welch Paul P.H. Wilson University of South Carolina, Nuclear Engineering Program, Columbia, SC 29201 University of Wisconsin - Madison, Department of Nuclear Engineering and Engineering Physics, Madison, WI 53706 University of Texas - Austin, Department of Mechanical Engineering, Nuclear and Radiation Engineering Program, Austin, TX 78758 University of California - Berkeley, Department of Nuclear Engineering Berkeley, CA 94720

The current state of nuclear fuel cycle simulation exists in highly customized form. Satisfying a wide range of users requires model modularity within such a tool. Cyclus is a fuel cycle simulator specifically designed to combat the lack of adaptability of previous generations of simulators. This is accomplished through an agent-based infrastructure and treating time discretely. The Cyclus kernel was developed to allow for models, called archetypes, of differing fidelity and function depending on need of the users. To take advantage of this flexibility, a user must write an archetype for their desired simulation if it does not yet exist within the Cyclus ecosystem. At this stage, a user graduates to the title of archetype developer.

Without automation, archetype development is difficult for the uninitiated. This paper presents the framework developed for simplifying the writing of archetypes: the Cyclus preprocessor, or cycpp. cycpp addresses the computer science and software development aspects of archetype development that can be addressed algorithmically, allowing the developer to focus on modeling the physics, social policies, and economics. cycpp passes through the code three times to perform the following tasks: normalizing the code via the C preprocessor, accumulation of notations, and code generation. Not only does this reduce the amount of code a developer must write by approximately an order of magnitude, but the archetypes are automatically validated.

fuel cycle, simulation, software

1 Introduction

Cyclus cyclus_v1_0 (); cyclus_v1_2 () is the first truly agent-based jennings2000agent () fuel cycle simulator. New technologies, while exciting, often pose unforeseen challenges. Cyclus is no exception to this rule. This paper answers the questions, “What precisely is an agent in a fuel cycle context?” and “What features of simulation can be abstracted away to ease the burden on fuel cycle researchers?”

The genesis of Cyclus lies in the desire to treat mass balances as discrete, model facilities individually rather than as a fleet, and to be able to quantitatively compare the effects of changing the fidelity of the facilities themselves. These goals imply a large degree of sophistication on the part of the simulator infrastructure. Resource exchange must be handled in a generic and dynamic way as opposed to being hard-coded for specific commodities. Simulations must be inherently comparable, which involves storage infrastructure that is designed around this need. Agents must be able to communicate with one another and learn about the environment in which they exist. Additionally, agents must be able to be dynamically deployed and the set of available agent models may not be collected until run time.

What sets fuel cycle simulation apart from traditional agent-based simulations is the high degree of agent specialization. Standard agent-based simulators are characterized as having a few types of agents, often only one and almost always less than five taylor2014agent (). The agent types are then specialized when they are instantiated in situ. This model is not appropriate for fuel cycle applications. For example, it would be unwise to have a single facility model that represents both enrichment and reactors, called EnrichmentOrReactor, that decides via a switch how it behaves when it is deployed. It is much more natural to have two models, Enrichment and Reactor, that implement their own physics calculations independently.

Cyclus enables agent specialization along two separate axes. The first defines an agent as an entity that determines its role in the fuel cycle. There are three kinds of entities: regions that represent geographic and governmental concerns, institutions that manage other agents, and facilities that implement physics calculations and are usually in charge of resource management.

The other axis of agent specialization distinguishes among who writes the model, who sets up the model for potential use in a simulation, and who actually deploys concrete representations of the model. At the highest level are archetypes whose behavior is parameterizable. Archetypes are software implementations of physical, chemical, economic, and political models. For example, a Reactor archetype may be parameterized by a target burnup. Authors of these highly reusable models are known as archetype developers. Archetypes are in turn configured into prototypes. A prototype is a copy of the archetype but with all parameterizations set to concrete values. Hence, a Reactor with a burnup of 42 MWd/kg is a prototype. Configuring archetypes into prototypes is done by the Cyclus user in the input file. Configuration requires no underlying knowledge of how the archetype is implemented, though that often helps. Finally, when prototypes are copied and deployed in the simulation they become agents. This usage of the term ‘agent’ to mean the in situ object is consistent with other agent-based literature macal2005tutorial (). Agent deployment happens exclusively via Cyclus itself; manual deployment of agents is not allowed. Archetypes that wish to deploy agents must schedule their building and decommissioning.

Archetype development is one of the most difficult aspects of agent-based simulation. Physical models be determined, implemented, and validated. Moreover, this is where agents interface with the Cyclus kernel itself. The dynamism of agent-based simulation coupled with the compulsion to have traditional simulator features (such as restart and validation) creates a complex interface with the kernel. Archetype development would be much simplified if saving and loading from disk and communicating with other agents were never a concern, though such a simulator would be of marginal use. Due to these complexities, archetype development in Cyclus has historically been difficult. Obtaining a working archetype that performed no physics calculations from scratch would take novice developers upwards of two weeks effort. The complexities that lead to such a high bar are emblematic not just of Cyclus, but of any agent-based fuel cycle simulator.

Informal polling by the Cyclus team over the years showed that a new developer circa Cyclus v0.1 took 2+ weeks to get a working ‘do-nothing’ archetype. This is obviously too long because most researchers do not have two weeks of time ‘just to try something out.’ By Cyclus v0.3 the do-nothing development time had been reduced to approximately one business week. In Cyclus v0.4, this time became about 3 days. As of Cyclus v1.0, this finally was reduced down to 1 - 4 hours, which meets appropriate expectations for someone attempting Cyclus as a first time archetype developer.

These dramatic development time reductions were caused by two forces: clarification of the archetype abstraction and explicit tools to help with archetype creation. While the region-institution-facility hierarchy was established early on, the formulation of this hierarchy in an agent-based paradigm took much longer to firmly establish. Once this notion had been refined, attention turned to simplifying Cyclus archetype development. For a long time in the history of this simulator and its predecessors, such as Global Evaluation of Nuclear Infrastructure Utilization Scenarios, Version 2 (GENIUS)oliver_studying_2009 (), tools to help make archetypes were notable by their absence. The addition of archetype tools by the Cyclus core developers made archetype development significantly more efficient.

The archetype development tools provided by Cyclus must overcome a variety of technical hurdles in order to make archetype development accessible. These include, but are not limited to, the lack of reflection in the C++ programming language, the desire to support multiple database formats, automatic validation of input files, special mechanisms for handling resource exchange and inventory persistence, and the somewhat complex interface required to support the snapshotting and restart of simulations. Such concerns are basic to Cyclus operation but ancillary to the physics, chemistry, and economics being modeled by an archetype developer. The minutia should ‘just work’ since it is not a core part of a fuel cycle model.

This paper describes the strategies, efforts, interfaces, and implementations that considerably reduce the complexity an archetype developer must deal with directly. This has been found to reduce development effort for simple agents down to a couple of hours for novices. Expert archetype developers realize further reductions down to a couple of minutes. This has has been accomplished without sacrificing an iota of simulation fidelity. Since such problems proliferate throughout all possible simulators in the Cyclus category, the methods described here apply beyond Cyclus. Though such methods sometimes dive into computer science and agent-based modeling details, they are always implemented with the express goal of making fuel cycle simulation simpler, easier, faster, more expressive, and validated.

This paper proceeds by first providing a more detailed motivation in §2. Then, §3 describes methods and mindsets that are used to ease archetype development. Some of these are high-level design strategies, while others are software interfaces that provide the correct fuel cycle agent abstractions. §4 describes the underlying algorithms and usages for those methodologies, which also require concrete implementations. Lastly, §5 provides final remarks and illustrates potential future directions for Cyclus archetype development.

2 Motivations & Problem Statement

Agent-based modeling frameworks necessarily place the agent as the fundamental abstraction. This is true in Cyclus as well. However, many problems that are solved with an Agent-Based Modeling (ABM)approach are sufficiently represented by one or two agents taylor2014agent (). However, in nuclear fuel cycle simulations there is a proliferation of facility types that are distinct both conceptually and in the kinds of physical processes that they implement. While it would be possible to merge all facility types into a single, highly parameterized agent model, it would be unwise to do so. Facilities that model fundamentally different physics should not be combined into a single class. Not only is it more work to combine them but it is also less intelligible. The same reasoning applies to why it is not a good idea to merge the concepts of institutions and regions with that of facilities; the subject of the model is fundamentally distinct from other models and this separation of concerns should be maintained.

So unlike other agent-based frameworks, the modularity of Cyclus drives an ecosystem of archetypes. An archetype is an agent class that specifies how the agent should behave via its own implementation of physics, chemistry, economic, and social policies. Archetypes are parameterized only in ways that make sense to the policies that they implement. Extraneous policies are left to other archetypes. For example, a nuclear reactor would not be parameterized based on separation efficiencies capacity, that would be left for a reprocessing facility.

All archetypes are agents. They are able to communicate (through resource exchange) with all other agents and they have access to the same information about the environment in which they live. The archetype abstraction provides speciation of agents so that each archetype may fill its own fuel cycle niche.

Archetypes are an essential abstraction layered on top of the agent abstraction. Fuel cycle facility, region, and institution modelers should directly create archetypes rather than raw agents. Thus for people trying to create, use, and extend Cyclus agents, archetypes should be their entry and exit point. Because this concept is central to how Cyclus works, such users are known as archetype developers.

The archetype abstraction has the added advantage that archetype developers need only be specialists in the field of the archetype that they are developing. Someone who knowledgeable about gaseous centrifuges could design an enrichment facility. A person that studies deep geologic repositories could model a long-term storage facility. A reactor physicist could create a suite of archetypes for various reactor technologies. In this way, an ecosystem of archetypes from representative experts can be built up. Since one does not need to be an expert to use an archetype, a well-developed ecosystem will provide a huge benefit to everyone. The separation of concerns provided by the archetype abstraction maximizes quality over the entire fuel cycle modeling process.

Still, for any simulator to be successful its key abstractions must be both easily configured by users and easily modified by developers. If these activities are too difficult, the barrier to entry for new users and developers will be insurmountable in a reasonable time frame. Otherwise, potential new users and developers will walk away in confusion and frustration. For Cyclus, archetype development needs to have first-class support.

This paper discusses how the Cyclus code base has overcome the inherent limitations of its design goals in order to provide a fertile platform on which to model the nuclear fuel cycle. Such strategies can apply to any and all agent-based fuel cycle simulators, of which there is currently only Cyclus.

3 Methods & Strategies

Archetype development can be a daunting task on its own. For this reason, many fuel cycle simulators choose to supply only a limited corral of pre-built archetypes. This places the responsibility of creating an maintaining the archetypes with the authors of the simulator. When only pre-built archetypes are available, then this suite defines the scope of all possible fuel cycles that a user can model. If the scope is not broad enough for the needs of a user, then the simulator developer must expand the scope or lose the user. This can create a bottleneck because the number of users may increase while the productivity of the simulation developer remains constant.

Cyclus avoids such bottlenecks by empowering users to create and maintain their own archetypes independent of the development timeline of the Cyclus kernel. However, this modularity comes with its own costs. Being able to plug in user-created archetypes implies an Application Programming Interface (API)to which the archetype conforms. This is an additional burden to both nascent and experienced archetype developers that does not effect the underlying behavior or physics. Rather, a large percentage of the code for an archetype exists soley to satisfy the Cyclus APIand does not impact the physics, economics, or other domain concerns being modeled.

To mitigate the difficulties of writing archetypes, Cyclus must aid in overcoming the hurdle of interfacing with kernel itself. Additionally, to the extent possible, Cyclus should also provide tools that ease the implementation of the physics and desired behavior. A variety of strategies are used by Cyclus to ease archetype development:

  • Automatic Model Templating: By automatically inspecting and creating portions of archetypes, the overhead of adhering to the Cyclus APIis removed. This is performed via preprocessing archetypes and then applying limited code generation to the original model. Such activities also add limited reflection to the C++ models as needed, which is important for archetypes that wish to know about themselves.

  • Data Communication Protocol: Cyclus provides a common basis for archetypes to store and retrieve complex data in the database. This is achevied through the implementation of Cyclus-specific type system. This alleviates the need for archetype developers to invent and implement custom persistence solutions.

  • Validation: Archetypes use Extensible Markup Language (XML)schema to validate that their prototypes have been configured correctly. This ensures the users of an archetype are adhering to the contraints imposed by the developer.

  • Metadata Annotations: Archetypes have a standard place to store and retrieve both pre-defined and arbitrary metadata. This allows for archetype developers to communicate relevant information to tools outside of Cyclus (such as a visualization tool).

  • Model Location: Cyclus has a packaging system for archetypes and libraries of archetypes. This provides a standard mechanism for searching for and locating models. Furthermore, all archetype developers can uniquely specify their own archetypes without the fear of overlapping names. For example, two developers could each have a Reactor archetype, but they would exist in different packages and be disambiguated.

  • Markets are not Agents: In an agent-based methodology, the mechanism for communication between agents is not an agent itself. Thus in Cyclus, market resolution was moved to be solely in the purview of kernel. In order to transfer resources, agents communicate in a well-defined way. Thus, archetype development need not include markets that specify how archetypes wish to communicate.

Though the above mechanisms are discussed with respect to Cyclus, they are transferable to any agent-based modeling framework that requires modular agent archetypes. The following subsections present greater detail regarding these strategies.

3.1 Automatic Model Templating

Every Cyclus archetype is required to implement the member functions seen in Table 1 and may optionally implement those seen in Table 2. Due to object orientation in C++ and how Cyclus stores state, these member functions must be implemented directly on the archetype itself. The implementation of these functions that archetypes inherit from the Agent class is not and cannot be sufficient.

Function Description
InfileToDb() Reads the prototype in the input file (XML format) and adds them to the initial startup database.
InitFrom(Db) Initializes a new agent or prototype from the database.
InitFrom(Agent) Iniializes a new agent or prototype from another agent or prototype.
InitInv() Initializes any starting inventory buffers.
Clone() Copies the current agent.
Snapshot() Stores the current state of the agent in the database.
SnapshotInv() Stores the current inventory buffers in the database.
schema() Returns the schema that user input must validate against.
annotations() Returns all metadata that is automatically gathered and supplied by the archetype developer.
Table 1: Required Archetype Interface
Function Description
Build() Called when the agent has been built.
EnterNotify() Allows for the agent to register for services.
BuildNotify() Informs when children of this agent have been built.
DecomNotify() Informs when children of this agent are about to be decommissioned.
Decommission() Removes the agent from the simulatuon.
Table 2: Optional Archetype Interface

Archetypes store state as public or private member variables directly on the class. For example, a Reactor archetype class could have a burnup declared as ‘double burnup;’. Not every agent has a burnup (e.g., an enrichment facility) and so the burnup member should not be part of Agent. Furthermore, archetypes are modularly defined. Because Cyclus cannot know all possible field names for all possible archetypes for all time, it can only react to how archetypes are written. In a dynamic language, the Agent superclass would still be able to to inspect instances of its subclasses to discover field names at runtime. Such introspection is called reflection. This would allow Agent to hold a single, generic implementation of each of the member functions in Listing 1, relieving archetype developers from having to implement them manually.

However, C++ lacks reflection. Neither Agent nor archetypes are allowed to dynamically discover what their member variable names are at runtime. This implies that the archetype developer must explicitly code in the appropriate variable names in the correct way for each of the nine required functions. For instance, the Reactor class must explicitly save the burnup member in the Snapshot() function if burnup is to be saved to the database. None of the nine required interfaces comes along automataically and minor typos could cause large breakages. For example, misspelling burnup as bunrup could cause the Snapshot() method to fail silently if it occured in the wrong location.

Since implementing this part of the archetype interface is both highly error-prone and routine, it is ripe for automatic code generation. Code generation replaces the tedious task of writing the required member functions with software that will insert such member functions into an otherwise fully developed archetype.

The code generation strategy has some limitations. First, it must be performed to prior to compilation. Second, the code generator must be provided with enough information about the archetype in order to accurately create the function implementation. Third and finally, it is highly desirable to keep archetypes in valid C++, rather that a special code generation language created just for Cyclus. Templating languages such as Jinja ronacher2011jinja2 () or any other variety of custom solutions would allow for expressive code generation. However, such template languages would be yet another tool for the archetype developer to learn. This runs counter to the goal of simplifying development.

The limitations above are all elegantly addressed through the use of a Cyclus-aware preprocessor. The first stage of C/C++ compilation is the C Prepocessor or cpp stallman1987c (). This tool is responsible for expanding #include directives and implementing other # directives, such as #pragma. It is executed prior to any other stage of compilation (lexing, parsing, etc.). Importantly, the #pragma directive is skipped by cpp if it is not recognized and the directive is passed though to further preprocessors or a C++ compiler. It is a purposeful hook for other preprocessors to use and implement their own code generation. If an alternative preprocessor only uses #pragma directives as its interface, the developer will be able to write in pure C++ and reap the benefits of an extra code-generation step.

However, all code generators must be supplied with sufficient information about where and how to create the code. These tasks may also be accomplished through the use of pragmas. To handle a suite of such utilities, a custom preprocessor is needed.

Certain pragmas may be used to parse only the needed information about an archetype, rather than parsing the entire class. For an archetype, the member variables that are saved and loaded from its instances are the most important. This is because they fully describe the state of an agent at all points in the simulation. These member variables are known as state variables. To generate the appropriate input and output routines for an archetype, at a minimum, the names and C++ types of all state variables must be known. The gathering of all these state variables is is called state accumulation.

Still, other pragmas denote where to insert automatically generated code into the original file. This is the tedious part of achetypes communicating with the Cyclus kernel. Specifically, the member functions in Listing 1 ought to be created and inserted for the archetype developer, avoiding entirely the need to write them by hand.

The Cyclus preprocessor, called cycpp, handles all of the cyclus code generation and state accumulation. This tool only recognizes directives that begin with #pragma cyclus so as to uniquely distinguish it from other preprocessors. cycpp performs three complete passes through archetype code:

  1. Normalization of the source via the standard C preprocessor cpp

  2. Accumulation of state and other agent annotations from normalized code

  3. Code generation into original source

Importantly, any preprocessor that adds reflection must make at minimum two passes: discovery of what exists (state accumulation) and adding this information back to the class (code generation). Single-pass preprocessors such as the standard cpp utility are not sufficient to enable reflection because they cannot guarantee that all relevant class information has been seen when code generation begins. Thus, cycpp includes these two passes plus an additional initial pass to simplify state accumulation. Further passes could be added that implement reflection onto the generated code itself, but this is often unnecessary. Particularly in Cyclus, further passes would be excessive since the portions of the cyclus::Agent interface that are generated are known ahead of time.

Cyclus-specific pragmas are broken up into two categories depending on whether they are most relevant to the state accumulation or code generation steps. They are denoted as annotation directives and code generation directives, respectively.

The cycpp annotation interface has two main directives:

  • #pragma cyclus var <dict> - state variable annotation

  • #pragma cyclus note <dict> - agent annotation or note

The state variable annotation is used on the line immediately above an archetype member variable to declare it as a state variable. The note directive is used anywhere in an archetype class declaration and applies to the archetype itself. Both of these have a <dict> argument that is a Python dictionary. This holds metadata about the state variable or the archetype. For example, a flux state variable declaration is shown in Listing 1.

#pragma cyclus var {"default": 42.0, "units": "n/cm2/s"}
double flux;
Listing 1: Flux State Variable Annotation

The code generation interface in its simplest form occurs via the Cyclus prime directive, #pragma cyclus. This expression will generate the entire archetype interface and insert it in place of the pragma. More fine-grained code generation may be used by passing additional arguments. The signature for such targeted code generation may be seen in Listing 2. The first argument is one of decl, def, or impl representing interface declarations, definitions (the declaration and the implementation together), or implementations (just the body without the declaration) of the archetype member functions respectively. Lacking any further arguments, this will produce the desired code for all of member functions in Listing 1. Optionally, a member function name in all lowercase (i.e., inittodb rather than InitToDb) may be supplied to generate code for the given function alone. Lastly, in cases where cycpp cannot determine the archetype to apply the code generation for, such as in an implementation file (*.cc or *.cpp), the agent class name may be provided as a final parameter.

#pragma cyclus <decl|def|impl> [<func> [<agent>]]
Listing 2: Targeted Code Generation Directive Signatures

When the annotation and code generation directives are combined and expanded with cycpp, agents become much simpler to write. Archtype developers are then free to focus on their physics or economics algorithms. The base Cyclus infrastructure is largely removed from the concern of the archetype developer. For example, a simple reactor model may be completely implemented as seen in Listing 3. The barrier to creating new archetypes is much lower than compared to the hundreds of lines of code that this would require without cycpp.

class Reactor : public cyclus::Facility {
  Reactor(cyclus::Context* ctx) {};
  virtual ~Reactor() {};
  #pragma cyclus
  #pragma cyclus var {'default': 4e14, 'units': 'n/cm2/2'}
  double flux;
  #pragma cyclus var {'default': 1000, 'units': 'MWe'}
  float power;
  #pragma cyclus var {'doc': 'Are we operating?'}
  bool shutdown;
Listing 3: Simple Reactor Archetype

3.2 Data Communication Protocol

Related to the issue of how to snapshot and restart simulations is the issue of what fundamental data types are allowed to be saved and loaded natively by the simulation. For many physics simulators, primitive data types (i.e., float, int, and string) and arrays of these types are sufficient to express and evaluate the underlying equations. This handful of types is small enough that most simulators can handle them in an ad hoc manner. Furthermore, these types often align with the structure of most databases, allowing for easy translation between disk and memory.

Agent-based fuel cycle modeling, however, subsumes physical modeling frameworks. The types of data that are needed to naturally express many fuel cycle concepts do not fit into the standard ‘arrays of floats’ mindset. More sophisticated types are needed, such as maps and sets of primitive types. For example, a reprocessing facility needs to have a mapping from elements to separation efficiencies. To avoid hard-coding the elements into the archetype, the user should be able to state which elements are allowed for each separation. The correct data type in C++ for such information is std::map<int, double>. Any other representation, say an int array or a float array, would likely be converted to a map by the archetype itself.

Cyclus increases expressiveness of archetypes and reduces error from extraneous transcription by natively supporting its own extensible type system. Every type has its own unique integer identifier as well as a variable name corresponding to this type. The types of the state variables are given by corresponding C++ representations. Every database format may then choose which types in the type system it supports and how it implements them. All types have a static rank, or the number of variable length dimensions, they support. For example, int and double are both rank-0, while vector<float> is rank-1 due to vectors having arbitrary length. As an optimization, the archetype developer may also give a shape, or the maximum size along each dimension. The type system is extensible, allowing for expressiveness to grow and evolve with the needs of archetype developers.

This strategy represents a significant abstraction over the needs and usage of most other simulator technologies. This level of detail is required by Cyclus due to the dynamically loadable agents. Without a strong type system, state variables would only be minimally useful and archetypes would have to rely on out-of-simulator mechanisms to save and load their state.

3.3 Metadata Annotations

Metadata annotations are coupled with code generation. State variable annotations are provided by using the #pragma cyclus var directive. Annotations for the archetypes as a whole are given using the #pragma cyclus note directive, as specified in §3.1. Both of these directives take a dictionary as an argument and this mapping must have string keys.

Metadata serves an important purpose by communicating information to the Cyclus preprocessor, to the Cyclus kernel, and even beyond the simulation to analysis and visualization tools. Some metadata is automatically generated from the archetype declaration itself. This information is considered read-only and required. Other annotations are supplied by the archetype developers and are optional. Some keys, such as documentation, are highly recommended even though they are optional.

Any key may be supplied to the annotation directives. For most keys, the purpose of the entry is given entirely by the archetype developer. However, some keys are reserved and have special meanings in various contexts. Table 3 lists these keys for state variable annotations and Table 4 displays the reserved keys for #pragma cyclus note.

key meaning
type The C++ type. Read-only.
index State variable order-of-appearence, 0-indexed. Read-only.
default The default value for this variable that is used if otherwise unspecified by the user. The type of the value must match the type of the variable.
shape The shape of the data type. If present this must be a list of integers of a given length (rank). Specifying positive values will, depending on the backend, render this a fixed-length data type of the provided length. A value of -1 will retain the variable-length along that axis. Fixed-length variables are normally more performant and thus it is often better practice to specify a shape if possible. For example, a length-5 string would have a shape of [5] and a length-10 vector of variable-length strings would have a shape of [10, -1].
doc Documentation string.
tooltip Brief documentation string for user interfaces.
units The physical units, if any, as a string.
userlevel Integer (0 - 10) representing ease (0) or difficulty (10) in using this variable, default 0.
schematype The data type that is used in the schema for input file validation. This enables the user to supply just the data type rather than having to overwrite the full schema for this state variable. In most cases - when the shape is rank 0 or 1 such as for scalars or vectors - this is simply a string. In cases where the rank is 2+ this is a list of strings. Please refer to the XMLSchema Datatypes xml-datatypes () for more information.
initfromcopy Code string to use in the InitFrom(Agent* m) function for the state variable instead of automatic code generation.
initfromdb Code string to use in the InitFrom(QueryableBackend* b) function for this state variable instead of automatic code generation.
infiletodb Code strings to use in the InfileToDb() function for this state variable instead of automatic code generation. This is a dictionary of string values with the keys ‘read’ and ‘write’ that represent reading values from the input file writing them out to the database, respectively.
schema Code string to use in the schema() function for this state variable instead of automatic code generation. This is an REgular LAnguage for XML Next Generation (RelaxNG)string. This is usually coupled with infiletodb to ensure the custom schema is read into the database correctly.
snapshot Code string to use in the Snapshot() function for this state variable instead of automatic code generation.
snapshotinv Code string to use in the SnapshotInv() function for this state variable instead of automatic code generation.
initinv Code string to use in the InitInv() function for this state variable instead of automatic code generation.
Table 3: Special State Variable Annotations
key meaning
vars The state variable annotations. Read-only.
name C++ class name (string) of the archetype. Read-only.
entity String of the type of archetype based on which class it inherits from; cyclus::Region, cyclus::Institution, or cyclus::Facilityare given by ‘region’, ‘institution’, or ‘facility’, respectively. If the class inherits from cyclus::Agent but not the previous three the string ‘archetype’ is used. The string ’unknown’ is used if the class does not inherit from cyclus::Agent. Read-only.
parents List of string class names of the direct super-classes of this archetype. Read-only.
all_parents List of string class names of all the super-classes of this archetype. Read-only.
doc Documentation string.
tooltip Brief documentation string for user interfaces.
userlevel Integer (0 - 10) representing ease (0) or difficulty (10) in using this variable, default 0.
Table 4: Special Agent Archetype Annotations

With respect to cycpp, metadata enables the customization of code generation without the need to alter the preprocessor itself or create an entirely new code generator. This tailoring of cycpp is exemplified by keys, such as 'shape', 'schematype', and 'initfromcopy'. Still, other keys are generated by cycpp itself and are considered read-only. These include the all-important 'type', 'index', 'name', and 'parents' keys. The automatic creation of these keys minimizes human transcription error for the most important metadata. This is a core simplification of archetype development.

Metadata is similarly important for the Cyclus kernel. All metadata is directly available via the annotations() member function, which returns a JavaScript Object Notation (JSON)object (equivalent to a Python dictionary with string keys). Combined with the auto-generated read-only keys from cycpp, the metadata provides much needed reflection to the archetypes. Unlike most C++ classes, archetypes have runtime access to their own class names, their parent classes, and the names and types of their state member variables. Therefore, the archetype may make runtime decisions about how to behave based on how it is defined. The major current use for the limited reflection in archetypes is for agents to save and load themselves.

Lastly, metadata is useful beyond Cyclus itself. Annotation keys such as 'doc', 'tooltip', and 'units' are included to provide end-user documentation. The 'userlevel' and other keys signal how archetypes and state variables should be treated in downstream user interfaces Even keys, such as 'default', that might have a primary usage elsewhere may still be helpful beyond the scope of Cyclus kernel.

The #pragma cyclus var and #pragma cyclus note directives provide unambiguous locations for implementing and generating metadata annotations. Metadata being contained completely within archetype declarations increases the worth of both the metadata and the archetypes because there is a single source for information about archetypes. Additionally, this high degree of locality eases the creation of archetypes, enabled by the automatic discovery of the annotation keys.

3.4 Validation

When writing Cyclus input files, users configure archetypes into prototypes. Configuration is done by assigning all state variables to initial values. This is the principal mechanism by which information flows from users to archetype developers. Therefore, it is reasonable for archetype developers to ask, “Does what the user gave me make sense?” For example:

  • a flux state variable should not be negative

  • an integer variable should not receive the string “Toaster”

  • a vector representing an N-group cross-section should have exactly N elements

If the user were to not follow these rules, the input file would be break physical constraints, type constraints, or shape constraints, respectively. Such breaking of constraints must be an error and the simulation should not be allowed to run. These rules can be codified into the archetypes allowing the simulator to check that whether or not any input file adheres to the given constraints. This is known as validation and Cyclus implements it automatically to the extent possible. Input file validation occurs prior to any simulation.

Cyclus input files are written in XML, which may be validated against a known structure called a schema. The schema is itself XMLthat describes the layout, types, and attributes of the input it will validate. Cyclus provides a default schema that describes the overall structure of the input file.

Archetypes, however, are dynamically loaded and so schema for their state variables may not be predicted or preloaded. To ensure consistency, archetype schema must be loaded along with the archetype itself. It may be tempting to ignore the notion of archetype schema and not validate the state variables. Howevere, this would create a system where there is no contract between the user and the archetype developer. Even if an archetype developer implemented ad hoc validation to their own classes, users would not anticipate such restrictions. To avoid this, Cyclus requires that archetypes provide their own validation via the schema() member function seen in Listing 1.

To accomplish the above, the schemas must be written in a schema language, which happens to be a subset of XML. Thus the schema interface is two steps removed from the C++ that defines the archetypes. This provides additional cognitive load to the archetype developer as they now must learn two additional tools before writing an archetype. However, the schema for most state variables may be derived automatically from information known to the preprocessor: the name of the state variable, its type, and optionally its shape and size in the case of containers. Thus the schema() member function is auto-generated by cycpp and input validation is obtained for free.

XML-based schema are extraordinarily useful as a mechanism for validating types. For example, if the user provides a floating point number rather than an expected string, they should be alerted to this error immediately. Moreover, schema can also validate structure to assert that a variable has the right shape. A length-5 vector must be initialized with five elements.

However, semantic and physical meaning must be ascribed by the archetype developer. Giving meaning to state variables based on their name and C++ type alone is impossible to accomplish via an automated method. For example, that a variable named flux on a Reactor should not be negative comes from a physical understanding and not a computational one. Such meaning can and should be given by the archetype developer via metadata.

Metadata for physical validation amounts to modifications of the schema. There are two annotation keys that may be used to accomplish this. The first clarifies the type that the schema uses and is called 'schematype'. In the example of a group structure shown in Listing 4, the 'schematype' could be assigned a value of 'positiveInteger' rather than relying on the default 'int' type that permits negatives and zeros. Additionally, the metadata key 'schema' can be used to wholly replace the auto-generated schema for the state variable at hand. This key can be used to change the name of the state variable with respect to the schema or to make a variable optional.

#pragma cyclus var {'schematype': 'positiveInteger'}
int ngroups;
Listing 4: Physical Constraint Addition via ‘schematype’

Finally, Cyclus also allows for the circumvention of automatic schema generation. This provides another method for instilling semantic meaning into state variable annotations that does not rely on metadata annotations, although partial or complete circumvention of code generation will require more effort from the archetype developer. The fine-grained control afforded by hand-writing the schema() member function is performed by advanced developers and only when absolutely necessary due to insufficiencies in cycpp.

3.5 Model Location

In a robust ecosystem of archetypes, it is nearly guaranteed that different archetype developers will want to use the same name. No single person or organization can reasonably lay sole claim to generic terms such as reactor, source, sink, and other names. Simultaneously, the archetype developer should not be concerned with accidental name collision between their archetypes and archetypes of other past, present, and future developers. Furthermore, it is often useful in a simulation or development campaign to group similar or related archetypes together. Uniqueness and collection problems are simultaneously solved through a hardy package system.

Cyclus packaging is an organizational structure that defines where on the file system archetypes are installed to, how the Cyclus kernel will load installed packages, and how to uniquely identify an archetype in an input file. Archetypes are denoted with a three-part archetype specification. When spelled out, this is a colon-separated string with the following elements:

  1. a slash-separated (/) directory path,

  2. a library name, and

  3. an archetype name.

For example, my/path:mylib:MyAgent represents MyAgent living in mylib residing in the 'my/path' directory. More than just a simple spelling convention, this is a necessary tool for searching for and discovering archetypes on the machine of the user.

The path portion of the specification is relative to the CYCLUS_PATH. This is an list of directories on the machine that will be searched in order to find the archetype of interest. By default, CYCLUS_PATH contains the current working directory, the Cyclus install directory, and the Cyclus build directory. CYCLUS_PATH may also be modified as an environment variable, allowing the user to permanently or temporarily alter the Cyclus search behavior. Thus the path specification (e.g. 'my/path') is interpreted as a sub-directory of all of the directories on the CYCLUS_PATH. For a directory d1 on CYCLUS_PATH, if 'd1/my/path' does not exist then the search for the archetype will continue along with d2, and so on. The path portion may be an empty string, indicating that the library lives directly on the CYCLUS_PATH.

The library name is the dynamically loadable library file name that stores the archetype. This does not include the lib- prefix or the file extension, which is generally operating system-dependent. For example, on a POSIX system, a file named would receive the library name myagents in the archetype specification. If a library name is not specified, then it is assumed to be the same as the archetype name. If desired, a single path may hold many libraries and a single library may hold many archetypes. Thus, archetypes may be grouped together coarsely or finely, depending on the needs of the archetype developers.

The path and library names together allow for complete disambiguation of archetypes because they enforce an important degree of namespacing. It is unlikely that two well-designed libraries will overlap in both library and archetype name. Even if they overlap, one or both libraries may be placed in respective sub-directories and the path is used to establish uniqueness. This strategy for specifying archetypes ultimately removes confusion and error from both archetype developers and users alike.

3.6 Markets are not Agents

In early versions of Cyclus, the dynamic resource exchange algorithm that the kernel used was itself dynamically loadable. Such an algorithm was called a market and was categorized as an entity alongside regions, institutions, and facilities. Each commodity was traded in its own market, which was specified by the user in the input file.

Unlike the other entities, though, a market did not have agency. It could not communicate with other agents in the simulation because it was itself the method for agent communication. Furthermore, resource exchange is the keystone part of all fuel cycle simulators. Relegating such algorithms to live outside of the kernel lead to maintenance problems. It became difficult to ensure that all markets correctly supported the proper exchange interface, thus minimizing the value of modularity within Cyclus.

Therefore, the notion of markets as a simulation entity was removed. In their stead, dynamic resource exchange algorithms were brought into the core to guarantee exchange feasibility. Moreover, this enabled all commodities to trade through a single global exchange. The commodity itself automatically defines the sub-exchange graph in which the commodity participates. These sub-exchange graphs may be thought of as analogous to the markets, which were removed in order to simplify archetype development. Since markets did not initially have any agency, their removal did not affect the agent-based nature of Cyclus. Rather, market removal allowed archetypes to communicate through a common resource exchange interface.

In summary, the current interpretation of dynamic resource exchange eases the burden on archetype developers. Because the primary duty of the kernel is to provide generic and valid resource exchange algorithms, the archetype developer is not required to construct a custom exchange for each commodity an archetype trades. Furthermore, market removal from the kernel does not impinge on exchange solver availability or customization. Many exchanges may be provided via user-tuneable parameters. The only restriction is that the exchange algorithms must exist within Cyclus itself. This is not considered overly burdensome, because individuals seeking to write custom exchanges - arguably the most advanced task in Cyclus- have likely transitioned from being an archetype developer to also being a kernel developer.

4 Implementation

In §3, the strategies and interfaces that Cyclus uses to simplify archetype development were presented. These represent notions about the amount of information and prior knowledge that the archetype developer must have in order to write archetypes. If a particular strategy decreases the knowledge required by archetype developers then it is considered beneficial to implement.

However, methods that are more intuitive for new users to understand are often proportionately more difficult to implement. For example, playing or mastering the game tic-tac-toe is a vastly different effort than designing the game in the first place. This section describes the infrastructure of current Cyclus archetype development. This is relevant to other fuel cycle simulators that wish to adopt the same strategies that Cyclus implements. In particular, the implementation of the Cyclus preprocessor, the type system, input file validation, and metadata annotations will all be covered here.

4.1 The Cyclus Preprocessor

The Cyclus preprocessor, cycpp, is responsible for all metadata collection and code generation for archetypes. It is implemented as a small Python utility that is currently less than 2000 lines in a single file. It has no dependencies other than the Python standard library lutz2010programming (). It is thus light-weight enough to move around between code projects, if needed. For the scale of its responsibility, cycpp is extremely efficient.

The preprocessor implements the three passes detailed in §3.1: normalization via standard cpp, state variable annotation accumulation, and code generation. The cycpp tool must be run on all C++ header and source files that contain archetype code and the #pragma cyclus directives. Running cycpp on files without such directives will result in no changes to the original file. The first cycpp pass that runs the C preprocessor is a trivial subprocess spawn. Importantly, this ensures that cycpp detects the same include, macro definitions, and macro un-definitions that actual compiler will see.

The second pass, state accumulation, represents half of the work that cycpp performs. The results from pass one are fed into this pass and scoured for potentially relevant information about the archetypes present in the file. Thus, state accumulation may be thought of as a traditional parser that transforms tokens (lines of the C++ file) into a more meaningful in-memory data structure. As a parser, pass two may be implemented as a state machine mertz2003text (); wagner2006modeling ().

Pass two is represented in cycpp by the StateAccumulator class, a state machine that compares the output lines from the C preprocessor against a series of filters. If a line matches the expected structure for a filter, then the filter executes a transformation function on the line and no further filters are executed. If the line does not match any filters, then the line is allowed to pass through the StateAccumulator. The filter-transformation sequence can be thought of in analogy to a sphere of a given radius (a line of code) attempting to pass through concentric windows (the filters) of decreasing aperture, as illustrated in Figure 1. This first window where the sphere stops represents the transformation that is executed. This sphere is allowed to move through the system without being stopped.

Figure 1: The StateAccumulator class passes lines of C++ code through a series of filters, each of which may transform the information heretofore gathered by previous filters. This may be thought of analogous to a spheres of various radii traversing concentric windows. The spheres, or lines of code, stop when they cannot pass a window, or filter. This triggers the execution of the transformation function of just that filter.

The filters implemented for pass two of cycpp are described in Table 5, in order of decreasing precedence. The most important of these filters implement the #pragma cyclus directives that the archetype uses to communicate with the preprocessor. The pragma filters typically modify attributes of the StateAccumulator, such as the context, the execns (or execution namespace), the aliases set, and the namespaces. These represent the classes, types, aliases, and other information that defines the scope of the C++ code. Such information is necessary for accurately representing archetypes and their state variables.

Most pass two filters that do not implement a preprocessor directive instead aggregate information about the available types. The VarDeclarationFilter has the important job of determining the C++ type of state variables from the member variable declaration on the archetype class. However, the C++ type system is complex and allows for a number of programmer modifications prior to the type declarations:

  • types may be aliased to any number of alternative names,

  • template types are white-space insensitive,

  • scoping rules apply to new type names, and

  • other issues must be resolved to accurately and uniquely represent a C++ type.

This requires that cycpp implement relevant type handling simply to correctly spell the canonical type name. Thus the StateAccumulator class acts as its own type system and returns the canonical form of any type it knows about at all points during pass two of cycpp.

order filter description
1 ClassAndSuperclassFilter Accumulates the class name from a class declaration. Also stores the names of the superclasses from the declaration.
2 AccessFilter Sets the current access control level: public, private, or protected.
3 ExecFilter Implements the #pragma cyclus exec <code> directive that allows for the execution of arbitrary Python code. The results of this code are added to the context that evaluates other cycpp directives.
4 UsingNamespaceFilter Adds and removes a namespace from the current scope via the C++ using namespace statement.
5 NamespaceAliasFilter Implements namespace aliasing in the current scope.
6 NamespaceFilter Sets and reverts a new namespace scope.
7 TypedefFilter Adds a type alias to the current scope via the C++ typedef statement.
8 UsingFilter Removes scope from a type by adding an alias in the current scope via the C++ using statement.
9 LinemarkerFilter Interprets cpp linemarker directives in order to produce more useful debugging information in cycpp.
10 NoteDecorationFilter Implements the cycpp #pragma cyclus note <dict> directive by evaluating the contents of <dict> and adding them to the archetype annotations.
11 VarDecorationFilter Implements the cycpp #pragma cyclus var <dict> directive for state variable annotations by evaluating the contents of <dict> in the current context and queuing them for the next state variable declaration.
12 VarDeclarationFilter State variable declaration. Applies the results of the immediately prior VarDecorationFilter as the state variable annotations. Furthermore, this filter parses out the name of the state variable, its index with respect to other state variables on this class, and resolves its C++ type into an unambiguous form.
13 PragmaCyclusErrorFilter Throws errors if #pragma cyclus directive is incorrectly implemented. This moves errors from happening at compile or run time to cycpp.
Table 5: Cyclus Preprocessor Pass 2 Filters (Higher order filters have lower execution precedence)

In cycpp, the only relevant type information is the name of the type. The concrete size in bits of a type and the operations that are available for that type are not directly relevant. This is because the primary purpose of the type of a state variable is to be able to fill in the appropriate values in the third pass.

The canonical form of a type has the following spelling rules:

  • Primitive types (int, double, std::string, etc.) and classes (cyclus::Blob, etc.) are spelled with strings of the names.

  • Template types (std::vector, std::map, etc.) are spelled with lists of length of the number of template parameters plus one. The first element of the list is a string that represents the template type (e.g. std::pair). The remaining elements of the list represent the template parameter types, in order, and may be either strings or lists. For example, the type std::map<int, std::vector<double>> would have the canonical form of ['std::map', 'int', ['vector', 'double']].

  • All namespaces must be included in the type name.

  • Pointer and reference types are not allowed because these may not be represented in the database.

The above rules create an accurate and language-independent mechanism for spelling C++ types, including templates. The preprocessor is aware of the following types that may be present in a Cyclus database in various combinations:

  • Primitives: bool, int, float, double, std::string

  • Known Classes: cyclus::Blob, boost::uuids::uuid, cyclus::toolkit::ResBuff, cyclus::toolkit::ResMap

  • Templates: std::vector, std::set, std::list, std::pair, std::map

Resolving a canonical type name is necessarily a recursive process. This is because aliases may point to other aliases — not just primitive type names. Thus to resolve an alias, one must walk through an arbitrarily deep graph of aliases to find the associated primitive. For example, given that myfloat points to float (the primitive) and mynumber points to myfloat, if a state variable was declared as myfloat only one alias lookup would be required whereas two would be required if it was declared as mynumber. The canonical form for all float, myfloat, and mynumber would all be float. This is what cycpp should record. Templates must recursively determine the template type name and the types of all template parameters. The canonical form of a type must be automatically computed to avoid an entire class of typographic errors by the archetype developers.

Aside from the type system semantics, pass two represents a relatively straightforward process of building up archetype information for later use. This later use occurs during code generation in pass three of cycpp. Conceptually, pass three is a more complex process than pass two because it must implement all of the member functions in Listing 1. In practice however, the body of each of these member functions follows its own pattern with respect to the state variables. Therefore, implementing pass three is significantly easier.

Much like pass two, pass three is also a state machine. The class that implements it is called CodeGenerator and the filters within this class implement the corresponding code generation routines. While the CodeGenerator does reuse some meta-data accumulation filters, it largely relies on the results of pass two for archetype and state variable information. The only data that cannot be reused and is recomputed is that which pertains to the scope of each line of C++ code.

Pass three traverses all lines of the source code for a third time. On this pass, the CodeGenerator will replace certain #pragma cyclus directives with the generated implementations. Pass three may act on the output of cpp, the results of pass one. However, it is more common for this to act on the original source and header files. This requires that the archetype developer write in mostly normative C++ and not abuse the C preprocessor. They must avoid double include errors and other downstream issues with compilation. The results of pass three, therefore, are a new version of the archetype source code that differs only in that it contains automatically implemented member functions.

Table 6 displays the filters that the CodeGenerator employs in order of precedence. These filters overlap somewhat with those of the StateAccumulator. This enables the efficient reuse of filters between state machines.

order filter description
1 InitFromCopyFilter Implements code generation for copy-constructor-like InitFrom() member function. This may be called with the #pragma cyclus [def\|decl\|impl] initfromcopy [classname] directive.
2 InitFromDbFilter Implements code generation for database constructor InitFrom() member function. This may be called with the #pragma cyclus [def\|decl\|impl] initfromdb [classname] directive.
3 InfileToDbFilter Implements code generation for the InfileToDb() member function that converts an input file into its database representation. This may be called with the #pragma cyclus [def\|decl\|impl] infiletodb [classname] directive.
4 CloneFilter Implements code generation for the Clone() member function that clones prototypes. This may be called with the #pragma cyclus [def\|decl\|impl] clone [classname] directive.
5 SchemaFilter Implements code generation for the schema() member function that returns the RelaxNGschema of the archetype for input file validation. This may be called with the #pragma cyclus [def\|decl\|impl] schema [classname] directive.
6 AnnotationsFilter Implements code generation for the annotations() member function that returns the archetype metadata that was compiled during cycpp pass two. This may be called with the #pragma cyclus [def\|decl\|impl] annotations [classname] directive.
7 InitInvFilter Implements code generation for the InitInv() member function that sets the initial resource inventories of the agent. This may be called with the #pragma cyclus [def\|decl\|impl] initinv [classname] directive.
8 SnapshotInvFilter Implements code generation for the SnapshotInv() member function that writes inventories to the database. This may be called with the #pragma cyclus [def\|decl\|impl] snapshotinv [classname] directive.
9 SnapshotFilter Implements code generation for the Snapshot() member function that writes state variables to the database. This may be called with the #pragma cyclus [def\|decl\|impl] snapshot [classname] directive.
10 ClassFilter Sets the current class name and scope.
11 AccessFilter Sets the current access control level, either public, private, or protected.
12 NamespaceAliasFilter Implements namespace aliasing in the current scope.
13 NamespaceFilter Sets and reverts a new namepsace scope.
Table 6: Cyclus Preprocessor Pass 3 Filters, higher order filters have lower execution precedence.
order filter description
14 VarDecorationFilter Implements the cycpp #pragma cyclus var <dict> directive for state variable annotations by evaluating the contents of <dict> in the current context and queuing them for the next state variable declaration.
15 VarDeclarationFilter State variable declaration. Applies the results of the immediately prior VarDecorationFilter as the state variable annotations. Furthermore, this filter parses out the name of the state variable, its index with respect to other state variables on this class, and resolves its C++ type into an unambiguous form.
16 LinemarkerFilter Interprets cpp linemarker directives in order to produce more useful debugging information in cycpp.
17 DefaultPragmaFilter Implements the default code generation directive, #pragma cyclus [def\|decl\|impl]. This calls the other code generation filters to obtain member function implementations.
18 PragmaCyclusErrorFilter Throws errors if #pragma cyclus directive is incorrectly implemented. This moves errors from happening at compile or run time to cycpp.
Table 7: Cyclus Preprocessor Pass 3 Filters (part 2).

When all of the pieces of cycpp are brought together, the benefits scale as the number of state variables times the number of code generated member functions (currently nine). This implies roughly an order of magnitude savings on the number of lines that an archetype developer must write per state variable. Moreover, exponential savings come from the fact that the archetype developers do not need to understand the details of the Cyclus interface. Even for a developer who knows the Cyclus interface completely, there is still a factor of ten less code to write. Consider again the simple Reactor example presented in Listing 3. These twelve lines of code are transformed into 112 lines by cycpp, the results of which are shown in Listing 5.

class Reactor : public cyclus::Facility {
  Reactor (cyclus::Context* ctx) {};
  virtual ~Reactor() {};
  virtual void InitFrom(Reactor* m) {
    flux = m->flux;
    power = m->power;
    shutdown = m->shutdown;
  virtual void InitFrom(cyclus::QueryableBackend* b) {
    cyclus::QueryResult qr = b->Query("Info", NULL);
    flux = qr.GetVal<double>("flux");
    power = qr.GetVal<float>("power");
    shutdown = qr.GetVal<bool>("shutdown");
  virtual void InfileToDb(cyclus::InfileTree* tree, cyclus::DbInit di) {
    tree = tree->SubTree("config/*");
    cyclus::InfileTree* sub;
    int i;
    int n;
    flux = cyclus::OptionalQuery<double>(tree, "flux", 4e+14);
    power = cyclus::OptionalQuery<float>(tree, "power", 1000);
    shutdown = cyclus::Query<bool>(tree, "shutdown");
    ->AddVal("flux", flux)
    ->AddVal("power", power)
    ->AddVal("shutdown", shutdown)
  virtual cyclus::Agent* Clone() {
    Reactor* m = new Reactor(context());
    return m;
  virtual std::string schema() {
    return ""
      "    <element name=\"flux\">\n"
      "        <data type=\"double\" />\n"
      "    </element>\n"
      "    <element name=\"power\">\n"
      "        <data type=\"float\" />\n"
      "    </element>\n"
      "<element name=\"shutdown\">\n"
      "    <data type=\"boolean\" />\n"
  virtual Json::Value annotations() {
    Json::Value root;
    Json::Reader reader;
    bool parsed_ok = reader.parse(
      ":\"float\",\"index\":1},\"shutdown\":{\"doc\":\"Are we "
      "operating?\",\"type\":\"bool\",\"index\":2}}}", root);
    if (!parsed_ok) {
      throw cyclus::ValueError("failed to parse annotations for Reactor.");
    return root;
  virtual void InitInv(cyclus::Inventories& inv) {
  virtual cyclus::Inventories SnapshotInv() {
    cyclus::Inventories invs;
    return invs;
  virtual void Snapshot(cyclus::DbInit di) {
    ->AddVal("flux", flux)
    ->AddVal("power", power)
    ->AddVal("shutdown", shutdown)
  #pragma cyclus var {'default': 4e14, 'units': 'n/cm2/2'}
  double flux;
  #pragma cyclus var {'default': 1000, 'units': 'MWe'}
  float power;
  #pragma cyclus var {'doc': 'Are we operating?'}
  bool shutdown;
Listing 5: Simple Reactor Archetype After Preprocessing with cycpp, line marker directives have been removed for space

Of course, archetypes may be much more complex than the Reactor example. This archetype does not participate in resource exchange, take advantage of the reflection features, use available annotations, or have more than a handful of state variables. Yet, even here, the value of a code generating preprocessor is readily apparent.

4.2 Database Backends & Types

Cyclus transparently supports a potentially limitless number of different database backends. Currently, two reference backends exist: Structured Query Lite (SQLite)owens2006definitive () and Hierarchical Data Format version 5 (HDF5)folk2011overview (). These two represent relational and hierarchical databases, respectively, and have different underlying design philosophies. Future formats that could be supported include plain text Comma-Separated Value (CSV)files or JSON. Given the wide range of potential uses cases, Cyclus must be able to execute based on only the feature set that is common among these formats. Features that are not available in a single format must either be provided by Cyclus itself or become optional in the backend interface.

The type system and reflection provided by cycpp allow archetypes to represent themselves in the database. Though this reflection can be taken advantage of and used elsewhere, it was initially implemented because of the need to restart a simulation. The database model extends well beyond the needs of the archetypes alone by serving as the fundamental on-disk representation for all Cyclus input and output.

Cyclus databases follow these fundamental abstractions:

  • All data are stored in tables with named columns,

  • Tables live in a flat hierarchy,

  • Columns may have any type described by the Cyclus type system, and

  • All tables must have a SimId column which uniquely and universally identifies the simulation.

Therefore, common databases notions such as the shape of a column, raw arrays, or queryability must be optional, omitted, or implemented inside the backend itself. Queryability is the most important, and is available in both HDF5and SQLite. If a database format or its backend lacks queryability (such as CSV), then it is impossible to start or restart a Cyclus simulation from it. Though, such a format may be used in conjunction with another, queryable format.

The database backends are deeply tied to the Cyclus type system. Types in Cyclus are represented by unique integers that map to C++ types by the enum called DbTypes. Simple types are represented by simple names: float becomes FLOAT, which is assigned to the identifier 2. Container types, such as vector, are more complex in that each template specification (vector<int>) has its own type in the Cyclus type system. Containers are further delineated as either fixed-length or Variable Length (VL). Thus even the relatively simple C++ type std::vector<int> receives two entries in the Cyclus type system: VECTOR_INT and VL_VECTOR_INT, which are given the identifiers 10 and 11. Thus the number of types in the Cyclus type system is obtained as 2 to the power of the rank or the total number of variable length parameters, including nettings. For example, the number of Cyclus types for std::map<int, std::string> is four (MAP_INT_STRING, VL_MAP_INT_STRING, MAP_INT_VL_STRING, VL_MAP_INT_VL_STRING) since both maps and strings may be variable length. Table 8 displays a sampling of types currently implemented in Cyclus. Each backend determines which types it wishes to support, though this must extend to a relatively robust subset in order to run even simple simulations.

id name C++ type rank
0 BOOL bool 0
1 INT int 0
2 FLOAT float 0
3 DOUBLE double 0
4 STRING std::string 1
5 VL_STRING std::string 1
6 BLOB cyclus::Blob 0
7 UUID boost::uuids::uuid 0
8 VECTOR_BOOL std::vector<bool> 1
9 VL_VECTOR_BOOL std::vector<bool> 1
10 VECTOR_INT std::vector<int> 1
11 VL_VECTOR_INT std::vector<int> 1
32 SET_STRING std::set<std::string> 2
33 VL_SET_STRING std::set<std::string> 2
34 SET_VL_STRING std::set<std::string> 2
35 VL_SET_VL_STRING std::set<std::string> 2
42 LIST_INT std::list<int> 1
43 VL_LIST_INT std::list<int> 1
57 PAIR_INT_INT std::pair<int, int> 0
104 MAP_STRING_STRING std::map<std::string, std::string> 3
105 VL_MAP_STRING_STRING std::map<std::string, std::string> 3
106 MAP_STRING_VL_STRING std::map<std::string, std::string> 3
107 VL_MAP_STRING_VL_STRING std::map<std::string, std::string> 3
120 MAP_VL_STRING_STRING std::map<std::string, std::string> 3
121 VL_MAP_VL_STRING_STRING std::map<std::string, std::string> 3
122 MAP_VL_STRING_VL_STRING std::map<std::string, std::string> 3
123 VL_MAP_VL_STRING_VL_STRING std::map<std::string, std::string> 3
Table 8: Sample Cyclus Types

A key database-enabling feature of the Cyclus type system is that the values of all types must be directly hashable using a cryptographic hash. The directness again implies that pointer and reference types are not allowed. For most database backends, indirection is not a supported feature. For those backends which do support indirection, such as HDF5and its linking mechanism, there is not a clear translation from indirection in memory to indirection on disk. Requiring hashable data types avoids several classes of errors entirely.

Hashability serves a dual role with respect to the backends. The first is that it provides a mechanism for uniquely identifying all elements of a type within reason. Cyclus uses the standard Secure Hash Algorithm 1 (SHA1)eastlake2001us () algorithm to compute hash values as 160-bit integers. Thus for types with a fixed bit width less than 160, such as int (typically 32-bits) or double (64-bits), every element is uniquely identifiable. For variable-length data types or very long types, the probability of a hash collision is only , which is approximately equal to . This is an astronomically small possibility, even over the course of billions of simulations. Thus, backends may use the hash to automatically de-duplicate data and store every unique value only once.

The second purpose for hashing is to allow backends to implement the storage of variable-length types as a bidirectional hash map using the SHA1as a key. This data structure is an associative array in which the values are uniquely determined from the keys and the keys are uniquely determined from the values. Furthermore, in Cyclus, the keys of this data structure are simply the hashes themselves. This differs from a typical hash map (e.g. Python dictionaries) in that they only require that values may be determined from the keys and only the keys must be unique. With a bidirectional hash map, knowing either the key or the value will provide the value or the key, respectively. The HDF5backend takes advantage of this data structure to store variable-length data in a 5-dimensional sparse array. The hash is chopped up into an array of five 32-bit unsigned integers that index into this sparse array. Then the hash is stored in the table and used to access the value in the corresponding sparse array for that type. This creates an efficient mechanism for storing vast amounts of potentially redundant variable-length data in a manner that mirrors the column storage for primitive types (bool, int, etc.). Since the hash is itself the index into a sparse array, the overhead from this lookup is minimal as compared with other parts of backend infrastructure.

Archetype developers may create their own custom tables in the database as well. This is done through using the backend interface directly in the archetype. Data that are fully dependent parameters of the archetype are not appropriate as state variables and thus should not be stored in this way. Custom tables have the same restrictions as other parts of the database as well as the additional restriction that they cannot reuse the table names that Cyclus itself uses. Writing to such tables is reserved for the kernel. Table 9 shows the standard tables generated by Cyclus. Distinct from the previously mentioned custom tables, the kernel will also produce tables whose names are based on the archetype specification for representing the archetype on disk. These tables are also reserved for the kernel alone.

name type description
Resources Table: Encodes a heritage tree for all resources. Because resources are tracked as immutable objects, every time a resource changes in the simulation (split, combined, transmuted, decayed, etc.), a new entry is added to this table. If two resources are combined, then the new resource entry will have the identifiers of the other two in its “Parent1” and “Parent2” columns. The Resources table does not encode any information about where a resource exists. This information can be inferred from the ResCreators and Transactions tables.
SimId UUID Simulation identifier
ResourceId INT The unique ID for this resource entry.
ObjId INT A resources object id (obj_id) as it existed during the simulation simulation.
Type VL_STRING One of “Material” or “Product”. These two types of resources have different internal state stored in different tables. If the type is product, then the internal state can be found in the Products table. If it is material, then it is in the Compositions table.
TimeCreated INT The simulation time step at which this resource state came into existence.
Quantity DOUBLE Amount of the resource in “kg” for material resources. Amount in terms of the specific quality for product resources.
Units VL_STRING “kg” for all material resources, “NONE” for product resources.
QualId INT Used to identify the corresponding internal-state entry (or entries) in the Products or Compositions table depending on the resource type.
Parent1 INT If a resource was newly created, this is zero. If this resource came from transmutation, combining, splitting, or decay then this is the parent ResourceId.
Parent2 INT If a resource was newly created, this is zero. If this resource came from transmutation, decay, or splitting, this is also zero. If the resource came from combining then this is the second parent’s ResourceId.
Compositions Table: Stores compositions. A composition consists of one or more nuclides and their respective mass fractions. Each nuclide within a composition has its own row but the same QualId.
SimId UUID Simulation identifier
QualId INT Key to associate this composition with one or more entries in the Resources table.
NucId INT Nuclide identifier in zzzaaammmm form.
MassFrac DOUBLE Mass fraction for the nuclide in this composition.
Recipes Table: Stores composition names.
SimId UUID Simulation identifier
Recipe VL_STRING Recipe name as given in the input file.
QualId INT Key to identify the composition for this recipe in the Compositions table.
Table 9: Standard Tables Reserved by the Cyclus Kernel, Columns given in order with names and types.
Products Table: Stores product information regarding quality.
SimId UUID Simulation identifier
QualId INT Key to associate this quality with one or more entries in the Resources table.
Quality VL_STRING Describes a product’s quality (e.g. “bananas”, “KWh”, etc.).
ResCreators Table: Stores instances of a new resource being created by an agent.
SimId UUID Simulation identifier.
ResourceId INT ID of a resource that was created during the simulation.
AgentId INT ID of the agent that created the resource associated with the ResourceId.
AgentEntry Table: Stores a row of information for each agent that enters the simulation.
SimId UUID Simulation identifier.
AgentId INT Every agent in a simulation gets its own, unique ID.
Kind VL_STRING Entity type. One of “Region”, “Inst”, “Facility”, or “Agent”.
Spec VL_STRING The single-string of the agent specification.
Prototype VL_STRING The prototype name, as defined in the input file, that was used to create this agent.
ParentId INT The AgentId of the parent agent that built or created this agent.
Lifetime INT Number of time steps an agent is designed to operate over. -1 indicates an infinite lifetime.
EnterTime INT The time step when the agent entered the simulation.
AgentExit Table: Stores a row of information for agents that leave a simulation. If this table does not exist, then no agents were decommissioned in the simulation.
SimId UUID Simulation identifier.
AgentId INT Key to the AgentId on the AgentEntry table.
ExitTime INT The time step when the agent exited the simulation.
Transactions Table: Every single resource transfer between two agents is recorded as a row in this table.
SimId UUID Simulation identifier.
TransactionId INT A unique identifier for this resource transfer.
SenderId INT AgentId for the sending agent.
ReceiverId INT AgentId for the receiving agent.
ResourceId INT Key to the entry in the Resources table that describes the transferred resource.
Commodity VL_STRING The commodity under which this transfer was negotiated.
Time INT The time step at which the resource transfer took place.
Table 10: Standard Tables Reserved by the Cyclus Kernel (cont.)
Info Table: Stores a row of information for each simulation that describes global simulation parameters and Cyclus dependency version information.
SimId UUID Simulation identifier.
Handle VL_STRING A user-specified value from the input file allowing for human identification of simulations in a database.
InitialYear INT The year in which time step zero occurs.
InitialMonth INT The month that time step zero represents.
Duration INT The length of the simulation in time steps.
ParentSimId UUID The SimId for this simulation’s parent. Zero if this simulation has no parent.
ParentType VL_STRING One of:
  1. “init” for simulations that are not based on any other simulation.

  2. “restart” for simulations that were restarted another simulation’s snapshot.

  3. “branch” for simulations that were started from a perturbed state of another simulation’s snapshot.

BranchTime INT Zero if this was not a restarted or branched simulation. Otherwise, the time step of the ParentSim at which the restart or branch occurred.
CyclusVersion VL_STRING Version of Cyclus used to run this simulation.
CyclusVersionDescribe VL_STRING Detailed Cyclus version info (with commit hash).
SqliteVersion VL_STRING SQLite version information.
Hdf5Version VL_STRING HDF5 version information.
BoostVersion VL_STRING Boost version information.
LibXML2Version VL_STRING libxml2 version information.
CoinCBCVersion VL_STRING COIN version information.
Table 11: Standard Tables Reserved by the Cyclus Kernel (cont.)
Finish Table: Stores one row of information for each simulation.
SimId UUID Simulation identifier.
EarlyTerm BOOL True if the simulation terminated early and did not complete normally. False otherwise.
EndTime INT The time step at which the simulation ended.
InputFiles Table: Stores the simulation input.
SimId UUID Simulation identifier.
Data BLOB A dump of the entire input file used for this simulation.
DecomSchedule Table: Stores information regarding when agents are scheduled to be decommissioned in the simulation. If a simulation ended before time reached the scheduled time, the agent would not have been decommissioned, but this table still includes the schedule information.
SimId UUID Simulation identifier.
AgentId INT ID of the agent that is to be decommissioned.
SchedTime INT The time step on which this decommissioning event was created.
DecomTime INT The time step on which the agent was (or would have been) decommissioned.
BuildSchedule Table: Stores information regarding when agents are scheduled to be built in the simulation. If a simulation ended before time reached the scheduled time, the agent would not have been built, but this table still includes the schedule information.
SimId UUID Simulation identifier.
ParentId INT The ID of the agent that will become this new agent’s parent.
Prototype VL_STRING The name of the agent prototype that will be used to generate the new agent. This corresponds to the prototypes defined in an input files.
SchedTime INT The time step on which this build event was created.
BuildTime INT The time step on which the agent was (or would have been) built and deployed into the simulation.
Snapshots Table: Stores entries containing information about every snapshot made during the simulation. All times in this table are candidates for simulation restart and branching.
SimId UUID Simulation identifier.
Time INT The time step a snapshot was taken for this simulation.
Table 12: Standard Tables Reserved by the Cyclus Kernel (cont.)

Though the database backend implementation and the associated type system may be complex to implement, its usage is mostly hidden to users and archetype developers through code generation. Even for complex template types, the Cyclus type system allows archetypes to be as expressive as needed to fit the model.

4.3 JSON Annotations

Archetype metadata annotation is an important part of Cyclus because it allows for reflection on the archetype classes. Well-defined metadata entries are described in Tables 3 & 4. Additionally, archetype developers may supply any other information and ascribe to it the semantics that they desire. This is done simply by adding undefined keys to the #pragma cyclus var and #pragma cyclus note cycpp directives. While this ensures that the metadata is robust to future changes and archetype developer customization, the annotations have implications for the Cyclus and archetype implementations.

Allowing for unknown metadata keys with unknown types for each value implies that the metadata is unstructured feldman2007text (). From a C++ implementation standpoint, this means that there is no class or struct that can be declared whose member variables encompass all possible metadata without at least one of those members being a pointer or reference. This is because determining the type of a blob of memory at runtime in C++ must use void*, char*, or other pointer indirection. Representing annotation in memory is more complex than in a single metadata class.

JavaScript Object Notationand its derivatives are largely acknowledged as sufficiently expressive formats for unstructured data moniruzzaman2013nosql (). This is because the JSONprimitives, which include integers, floats, strings, booleans, null, arrays, and objects (hash tables with string keys), are easily translatable into native data structures in most modern programming languages such as Python and C++. Furthermore, the JSONsyntax is concise and intuitive. XMLcould have been used as an alternative format, but a schema and the translation to native data structures would have to be handled manually. Yet-Another Markup Language (YAML)ben2009yaml () or Python itself offer more likely alternatives to JSONbut require a more sophisticated interpreters corresponding to their more powerful syntax.

JSONis a metadata representation that resides on disk, not in memory. Translation from plain text JSONto C++ data structures is performed via the JsonCpp software eltuhamy2014native (). This does the work of parsing JSONcode, implementing the JSONtype system, and translating back and forth between JSONtypes and C++ types. It provides a fully introspective container for arbitrary metadata called Json::Value. An instance of this class is precisely what the annotations() archetype member function returns. Therefore, the entire metadata workflow is as follows:

  1. Archetype developer writes metadata using annotation directives as a Python dictionary with string keys.

  2. cycpp parses, evaluates, and accumulates the annotations into a single metadata dictionary per archetype during pass two of preprocessing.

  3. Pass three of cycpp converts the metadata to a JSON-formatted string using JSONutilities in the Python standard library. This comprises the majority of the code generated for annotations() member function.

  4. When annotation() is called from C++, the JSONstring is parsed by JsonCpp and a new instance of Json::Value is returned that corresponds to the metadata.

In this way, JSONis used as an exchange format between Python and C++, between archetype developer and user, and between compile time and run time.

4.4 XML Validation

A key benefit to the Cyclus simulation infrastructure is the runtime guarantee of valid input files provided to both users and archetype developers. Developers are guaranteed valid construction of archetypes within a simulation, and users are notified immediately if a given input file would have resulted in invalid archetype construction. The processes required to provide such guarantees are implemented using robust schema validation with XMLand RelaxNGclark2001relax ().

For a given archetype, a developer defines the expected input structure in the schema() function manually or via the #pragma cyclus var preprocessor directive. Upon initiating a Cyclus simulation (i.e., at run time), a master schema is generated by combining the schema of all discovered archetypes on a given computing system and inserting the collection into a general Cyclus schema. The master Cyclus schema is used to define simulation-level input as well as general entity input. For example, all cyclus::Facility archetypes have input parameters common to the cyclus::Facility entity, e.g., a name and a lifetime, and input parameters specific to their archetype. Listing 6 shows a section of a generated Cyclus master schema pertaining to the cyclus::Facility entity input on a computing system on which archetypes named Reactor, Source, and Sink were installed. Listing 7 shows the generated schema for the simple Reactor archetype discussed in section §3.1.

  <element name="facility">
    <element name="name">
      <element name="lifetime">
        <data type="nonNegativeInteger"/>
    <element name="config">
        <ref name="Reactor"/ >
        <ref name="Source"/ >
        <ref name="Sink"/ >
Listing 6: Generated Cyclus Facility Schema for a Computing System with Reactor, Source, and Sink Archetypes Installed
<element name="Reactor">
      <element name="flux">
        <data type="double" />
      <element name="power">
        <data type="float" />
    <element name="shutdown">
      <data type="boolean" />
Listing 7: Generated Simple Reactor Schema

After generating master Cyclus schema, user input is provided to an instance of the cyclus::RelaxNGValidator class. This class utilizes the C++ libxml2 library to validate the user input against the generated RelaxNGschema.

If input validation is successful, the defined simulation is then instantiated and executed. A section of valid input for the Reactor is shown in Listing 8. Note that because the <optional> tag is utilized in the schema, not all parameters are required to be specified. Furthermore, default values defined in the Reactor #pragma cyclus var annotations are used for the unspecified parameters.

Listing 8: A Valid Input Snippet for the Simple Reactor

If the input is determined to be invalid, an error is raised without beginning the simulation. Listing 9 shows an example of input for the Reactor that is invalid because the power input parameter type is not a float; Cyclus fails immediately with the error message shown in Listing 10.

Listing 9: An Invalid Input Snippet for the Simple Reactor
Entity: line 23: element capacity: Relax-NG validity error : Type double doesn't allow value 'magic'
Entity: line 23: element capacity: Relax-NG validity error : Error validating datatype double
Entity: line 23: element capacity: Relax-NG validity error : Element power failed to validate content
 ERROR(core  ):Document failed schema validation'
Listing 10: A Cyclus Error Message from the Invalid Input in Listing 9

5 Conclusions

Writing archetypes can be a daunting task because reasonably accurate models require knowledge of physics, economics, and computer science to solve a single nuclear engineering problem. Unlike other spheres of nuclear engineering, decoupling these domains from one another is often not possible without significant simplification. Cyclus is no exception to this and is designed to allow for complete fidelity throughout all aspects of the simulation. The advantage of the Cyclus design is that it enables full modeling fidelity without requiring that archetype developers actively address every class of problem every time they pursue a new archetype.

Cyclus succeeds in simplifying archetype development by identifying a category of computer science and software development problems that are addressed algorithmically. This moves effort away from humans, who are pursing physics and economics, and onto computers. This automation happens by default for archetype development and reduces manual code writing by approximately 10 times. Additionally, the automation may be partially or fully reduced if the default generated code is not desired.

The Cyclus system enables better fuel cycle simulations by creating better archetypes. Improved archetypes are a direct consequence of two features of the preprocessor. First, Cyclus encourages developers to write the archetype that they intended to implement. Secondly, the archetypes are automatically validated.

State variables are easy to create. When a software feature has a high cost to use, developers will minimize the number of times that they invoke it. This can sometimes lead to sacrificing model fidelity in an effort to author more concise code. However, the long-term completeness of an archetype with respect to its physics calculations should not be based, even in part, on the short-term impetus to have a minimum-viable product. By dramatically reducing the length of time it takes to implement a state variable, archetype developers implement more state variables and thus more precise and tunable models.

Furthermore, automatically generating archetype code removes typographic errors and Cyclus interface misuse. This avoids potential and frustrating problems in archetype development. The generated code derives its validity from cycpp, which itself is extensively tested. Any errors accidentally introduced by cycpp would be endemic to all archetypes, but a fix to cycpp would be the corresponding solution. Archetypes are thus partially vetted due to cycpp.

The preprocessor also generates schema for archetypes. This provides a mechanism for automatically validating user input. Without validation, the archetype developer has no guarantee that the user has entered a meaningful or physically possible value (e.g., negative fluxes). Rather than approaching this problem in an ad hoc manner, the Cyclus interface demands that user input be examined via RelaxNG. The overhead of this requirement is mitigated since the archetype developer obtains the schema for free. This assures a high level of quality in using archetypes as well as developing them.

The strategies detailed and implemented in this paper radically reduce the overhead of writing archetypes. By enabling more expressibility and greater modifiability, developers and simulators are able to more easily experiment. Alternative fuel cycle representations may be explored quantitatively at an unparalleled rate.

However, archetype development tools and approaches are not without further potential refinements. cycpp will undergo continued improvement as more archetypes are developed and common usage patterns emerge. Codifying and auto-generating these patterns is a rich area of exploration. The authors anticipate that inventory and resource exchange patterns will be among the first targeted, which would likely take the form of new filters in pass three.

Furthermore, the fundamentals of the Cyclus type system will be used in perpetuity, as enabled by the extensibility of the type system. More types will be added as needed by the archetype developers. It is also possible to make the type system dynamic, allowing for custom types to be implemented at run time. This could be a boon to archetype developers seeking to create a wide variety of custom tables.

The preprocessor could also improve the generated code. Cyclus reserves the right to add additional metadata keys and associated meanings. For example, a 'range' key could specify the acceptable range for a state variable. This could in turn provide better validation by adding bounds checks beyond the what is performed by RelaxNG. A similar strategy could be followed for categorical variables whereby set membership would be verified. The code that is generated for future keys depends largely on the meaning ascribed to those keys. There is no limit to the richness of available metadata.

In summary, archetype development is has been made significantly easier. This is due in large part to the advent of the Cyclus preprocessor. While cycpp itself is the fruit of a large computer science and software development effort, it is used here primarily to improve fuel cycle simulations. Cyclus provides a solid ground as a platform for archetype development while simultaneously nimble enough to allow for future growth. Independent of Cyclus, the strategies and methods that Cyclus implements for archetype developers are translatable to any agent-based fuel cycle simulator. Some aspects, such as the type system, may even be exportable to general simulation science.


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