YAML simulation specification
Warning
This reference guide assumes that the reader knows the basics of YAML. A good resource to learn it quickly is Learn X in Y minutes where X = YAML
Reading this document
The key words MUST, MUST NOT, REQUIRED, SHALL, SHALL NOT, SHOULD, SHOULD NOT, RECOMMENDED, MAY, and OPTIONAL in this document are to be interpreted as described in RFC 2119.
Simulation document structure
The document MUST be YAML map.
The map MUST contain all the mandatory Alchemist keys,
MAY contain any subset of the optional Alchemist keys,
MAY contain any key whose name begins with underscore (_
),
and MUST NOT contain any other key.
The sets of valid cobinations of mandatory and optional keys for each section of the document is specified in form of Kotlin code as follows:
Types of entries
Type | Description |
---|---|
Any | Any YAML type |
Int | YAML integer number, or other type that can be parsed into an integer |
List | Any YAML List |
Map | Any YAML Map |
MultiSpec | A list of Spec. A Map matches a MultiSpec if it matches one and only one of its Spec. |
Number | YAML number |
Spec | Pair of lists of strings. The first list contains mandatory keys, the second optional keys. A map matches a Spec if it contains all its mandatory keys, any of the optional keys, and no other key |
SpecMap | A YAML Map matching a MultiSpec |
String | YAML String |
Traversable | One of: A SpecMap, a List of Traversable, a Map of Traversable |
Arbitrary class loading system
Type: SpecMap
Alchemist is able to load arbitrary types conforming to the expected interface
(or Scala trait
).
The expected type depends on where the class is requested.
This section describes how the system works independently of the specific target type.
(Multi)Spec
Mandatory keys | Optional keys |
---|---|
type |
parameters |
type
Type: String
The name of an instanceable class compatible with the expected interface. It can be either the qualified name or a simple name, in the latter case the class SHOULD be located in the same package where the default alchemist implementations of the same interface live.
If a name includes a .
, it is interpreted as a fully qualified name.
Otherwise, it is interpreted as a simple name.
Provided types SHOULD NOT be located in the default package.
For instance, if the expected type is an Action
and the concrete type FooAction
,
FooAction
SHOULD be located into package it.unibo.alchemist.model.actions
.
parameters
Type: List or Map
The list of parameters the constructor of type should be passed.
Alchemist automatically provides contextual information to the constructors:
for instance, if an Action
is being built,
the loading system is aware of the current
RandomGenerator
,
Incarnation
,
Environment
,
Deployment
,
Node
, TimeDistribution
, and
Reaction
,
as the action requires all of them.
Consequently, all parameters of these types SHOULD NOT be manually specified
(on the other hand, the syntax is built to make it very difficult to do by mistake).
The constructor MAY fail if they are provided.
If a Map is provided instead of a List, then the keys are interpred as the parameter names, and their associated values as the corresponding parameter values. Since Java 11 does not support named arguments, this special invocation type is built around the Kotlin reflection, thus, the concrete class whose constructor is being invoked MUST be written in Kotlin.
When using named arguments,
if at least one optional parameter is specified,
then all the previous optional parameters MUST be specified as well.
This limitation is due to the fact that Alchemist supports loading of JVM classes regardless of their origin language,
and, thus, the simulator must leverage constructor overloading to emulate optional parameters.
In the case of Kotlin classes, because of the way
@JvmOverloads
works, only a (reasonable) subset of all possible overloads gets generated, and they differ by parameter count.
Instantiation is delegated to the Java Implicit Reflective Factory.
Examples
- Construction of a
Point
- Construction of variables with named parameters
Counter-examples
- The following simulation fails on loading, as
BidimensionalGaussianLayer
has the first and last parameters marked as optional: in order to provide the latter, the designer must also provide the former.
Document root
Type: SpecMap
The document contents at the root of the file.
Contains all the information required to buld a
Loader
,
which, in turn, is able to spawn
Simulation
s
through a
Launcher
.
(Multi)Spec
Mandatory keys | Optional keys |
---|---|
incarnation |
deployments , environment , export , layers , launcher , network-model , remote-dependencies , seeds , terminate , variables |
Examples
- Minimal Biochemistry specification
- Minimal Protelis specification
- Minimal SAPERE specification
incarnation
Type: String
Valid incarnation types in the full distribution:
biochemistry
protelis
sapere
scafi
Examples
- Minimal Biochemistry specification
- Minimal Protelis specification
- Minimal SAPERE specification
action
Builds an Action
using the arbitrary class loading system.
condition
Builds a Condition
using the arbitrary class loading system.
deployments
Type: Traversable
Traversable of deployment
deployment
Type: SpecMap
Definition of the positions of a set of nodes.
Builds a
Deployment
using the same syntax of arbitrary class loading system,
with additional keys.
(Multi)Spec
Mandatory keys | Optional keys |
---|---|
type |
parameters , contents , nodes , programs |
Examples
- Deployment of a single node in a point
- Deployment of three nodes
- Deployment of three nodes, but nesting the traversable
- Deployment of three nodes through
SpecificPositions
. Grid
centered in(0, 0)
, with nodes distanced of0.25
both horizontally and vertically.- Irregular
Grid
centered in(0, 0)
, with nodes distanced of0.25
both horizontally and vertically, randomly perturbed of (±0.1
distance units). - Nodes located randomly inside a
Circle
- Nodes located randomly inside a
Rectangle
- Nodes located randomly inside a
Polygon
delimiting the Venice Lagoon
deployment.type
Same as type
deployment.parameters
Same as parameters
deployment.contents
Type: Traversable of content
deployment.nodes
Type: SpecMap
Forces the type of Node
, building concrete types through
the arbitrary class loading system.
If left unspecified, nodes get created through
Incarnation.createNode
.
Examples
- Creation of heterogeneous pedestrians
deployment.properties
Type: Traversable of property
deployment.programs
Type: Traversable of program
content
Type: SpecMap
Definition of the contents (Molecule
s and Concentration
s) of a group of nodes.
(Multi)Spec
Mandatory keys | Optional keys |
---|---|
molecule , concentration |
in |
Examples
- Three molecules injected into all nodes deployed in the scenario
- Injection of a molecule only in those nodes located inside a
Rectangle
content.molecule
Type: String or SpecMap
The name of the molecule to be injected.
If a String is provided, then it is created via Incarnation.createMolecule
.
Otherwise, the arbitrary class loading system SHOULD be used.
content.concentration
Type: String
The concentration of the molecule to be injected.
If a String is provided, then it is created via Incarnation.createConcentration
.
Otherwise, the arbitrary class loading system SHOULD be used.
content.in
Type: Traversable of shapeFilter
property
Type: SpecMap
(Multi)Spec
Mandatory keys | Optional keys |
---|---|
type |
parameters , in |
property.type
Same as type
property.parameters
Same as parameters
property.in
Type: Traversable of shapeFilter
environment
Type: SpecMap
Builds an Environment
using the same syntax of arbitrary class loading system.
If left unspecified, defaults to a bidimensional Euclidean manifold:
Continuous2DEnvironment
.
Type: SpecMap
Examples
- Default environment, omitted specification
- Explicitly builds a
Continuous2DEnvironment
solely with the contextual parameters - Explicitly builds a
Continuous2DEnvironment
using the qualified type name using only the contextual parameters - Explicitly builds a
Continuous2DEnvironment
explicitly specifying that no parameters but the contextual ones should be used
export
Type: Traversable of exporter
exporter
Type: SpecMap
Definition of the contents (Molecule
s and Concentration
s) of a group of nodes.
(Multi)Spec
Mandatory keys | Optional keys |
---|---|
type , data |
parameters |
exporter.type
Same as type
exporter.data
Type: Traversable of extractor
exporter.parameters
Same as parameters
extractor
Type: String or SpecMap
The only supported String is "time"
.
Otherwise, a SpecMap MUST be provided.
Creates instances of Extractor
.
(Multi)Spec
Mandatory keys | Optional keys |
---|---|
type |
parameters |
molecule |
property , aggregators , value-filter |
extractor.type
Same as type
extractor.parameters
Same as parameters
extractor.molecule
Type: String
Name of a Molecule
to be read from nodes and exported.
The String is passed down to Incarnation.createMolecule
.
The created molecule is read from every node.
extractor.property
Type: String
Name of a property to be extracted from the selected Molecule
.
The Molecule and the String are passed down to Incarnation.getProperty
.
The obtained value is added to the exports.
extractor.aggregators
Type: String or List of Strings
Name of any valid
UnivariateStatistic
,
case insensitive.
All those provided with Apache Commons Math are available by default.
New statistics can be defined,
they get loaded transparently as far as their package matches the one of Apache Commons Math.
If the aggregators are specified, only one value per aggregator gets exported, instead of one value for each node.
extractor.value-filter
Type: String or SpecMap
Builds a ExportFilter
,
to be applied to raw data before being processed by the aggregators
(#extractoraggregators),
if present.
If a String is provided, then it is used to load a policy from CommonFilters
.
Otherwise, the arbitrary class loading system MUST be used.
Mandatory keys | Optional keys |
---|---|
type |
parameters |
extractor.value-filter.type
Same as type
extractor.value-filter.parameters
Same as parameters
launcher
Type: SpecMap
Builds a Launcher
using the arbitrary class loading system.
If unspecified, defaults to DefaultLauncher
,
which runs the default simulation,
unless the variable set on which the batch should be executed is specified.
Customizing the launcher can be useful for implementing custom batch execution strategies, or “simulations of simulations”, if the process requires multiple simulation “stages” (e.g., running a batch to train a neural network, then running another batch to test it).
layer
Type: SpecMap
Builds a Layer
using the arbitrary class loading system.
Examples
- Creation of two
Layer
s - Creation of two
BidimensionalGaussianLayer
s:
layers
Type: Traversable of layer
Examples
- Creation of two
Layer
s - Creation of two
BidimensionalGaussianLayer
s:
monitor
Type: SpecMap
Builds a OutputMonitor
using the arbitrary class loading system.
Examples
- Creation of one
OutputMonitor
s
monitors
Type: Traversable of monitor
Examples
- Creation of one
OutputMonitor
s
network-model
Type: SpecMap
Builds a LinkingRule
using the arbitrary class loading system.
If unspecified, defaults to NoLinks
,
and no node will have any neighbor.
Examples
- Nodes connected when closer than some range
program
Type: SpecMap
Definition of the contents (Molecule
s and Concentration
s) of a group of nodes.
(Multi)Spec
Mandatory keys | Optional keys |
---|---|
type |
parameters , conditions , time-distribution actions |
program |
time-distribution |
program.type
Same as type
program.program
Type: String
Passed to Incarnation.createReaction
to be interepreted and
program.in
Type: Traversable of shapeFilter
program.actions
Type: Traversable of action
program.conditions
Type: Traversable of condition
program.parameters
Same as parameters
program.time-distribution
Type: String or SpecMap
Builds a TimeDistribution
.
If a String is provided, then it is created via Incarnation.createTimeDistribution
.
Otherwise, the arbitrary class loading system SHOULD be used.
remote-dependencies
shapeFilter
Type: SpecMap
Builds a PositionBasedFilter
using the arbitrary class loading system.
Examples
- Injection of a molecule only in those nodes located inside a
Rectangle
seeds
Type: SpecMap
Selection of the seed for the
RandomGenerator
s.
(Multi)Spec
Mandatory keys | Optional keys |
---|---|
scenario , simulation |
seeds.scenario
Type: Int
Selection of the seed for the
RandomGenerator
controlling the position of random displacements.
seeds.simulation
Type: Int
Selection of the seed for the
RandomGenerator
controlling the evolution of the events of the simulation.
terminate
Type: Traversable of terminator
terminator
Type: SpecMap
Builds a Predicate
using the arbitrary class loading system.
Examples
- Termination after some time
variable
Type: SpecMap
Definition of free and dependent variables.
(Multi)Spec
Mandatory keys | Optional keys |
---|---|
type |
parameters |
min , max , step , default |
|
formula |
language , timeout |
Variables can be created in three ways:
- Using the arbitrary class loading system
to produce an instance of
Variable
orDependentVariable
; - specifying the parameters of a
LinearVariable
(minimum and maximum values, incrementation step, and default value); - writing an expression that can be interpreted by some JSR-223-compatible language whose interpreter is in the
classpath, possibly specifying a timeout. Produces a
DependentVariable
.
variable.type
Same as type
variable.parameters
Same as parameters
variable.default
Type: Number
Default value for a LinearVariable
,
to be selected if the variable is not among those generating the batch.
variable.max
Type: Number
Maximum value for a LinearVariable
variable.min
Type: Number
Minimum value for a LinearVariable
variable.step
Type: Number
Size of the incremental step of a LinearVariable
variable.formula
Type: String
Code that can be interpreted by a JSR223Variable
.
variable.language
Type: String
Language to be used by a JSR223Variable
.
The language must be available in the classpath.
Groovy (default), Kotlin (kotlin
or kts
), and Scala (scala
) are supported natively.
variable.timeout
Type: Int
Time in milliseconds after which the interpreter of the
JSR223Variable
is considered stuck or in livelock.
The interpreter gets interrupted and the simulation loading fails to prevent unresponsive simulations.
Defaults to 1000ms.
variables
Type: Traversable of variable