Class Output

A list of the simulation'sexpected visualizations and reports.

InstanceTypeDescription
AgentNameWriterAgentNameWriter (Output)Maps each observed agent name to a unique numeric ID. Emits two files: a binary file containing vectors of name IDs by time, and a text file providing a mapping between numeric IDs and text names. Used, eg, for generating visualizations.
CensusWriterCensusWriter (Output)Census writer produces one tab-delimited file per simulation instance. Each row in the file corresponds to a time point, and the columns capture the number of agents of a given state (class) observed at that time. There is one column for each state observed through the course of the simulation.
ContinuumHistogramWriterContinuumHistoWriter (Output)ContinuumHistoWriter provides a histogram of solute concentrations at each time point recorded in each instance of the simulation. Data are reported in a tab-delimited text file, with one text file per simulation instance.
ContinuumStateWriterContinuumStateWriter (Output)Produces binary files containing frame-by-frame continuum value data for each continuum layer. The ContinuumStateWriter produces two files per continuum layer per simulation instance: one representing the overall state of the layer, and one capturing extremum metadata.
CoordinateIndexerCoordinateIndexer (Output)Produces a text-based file that specified a correspondence between every coordinate in the nanoverse.runtime.geometry and a unique integer index. The indexing algorithm used is common to all reports and is used internally within Nanoverse simulations. One file per instance.
CorrelationWriterCorrelationWriter (Output)Calculate the pairwise correlation between individuals at every distance. This calculation is used to measure spatial structure. The results are measured at a specified time point, and aggregated over all simulations.
HaltTimeWriterHaltTimeWriter (Output)HaltTimeWriter creates a single, tab-delimited text file, with each row containing the (simulation) time and cause of simulation halt for each instance run.
HighlightWriterHighlightWriter (Output)Highlights can be used to flag particular coordinates for special accents in visualizations. HighlightWriter produces files containing yes-or-no values for each location at each recorded time in a simulation. The writer produces one file per specified channel per instance.
IndividualHaltWriterIndividualHaltWriter (Output)null
InterfaceCensusWriterInterfaceCensusWriter (Output)Reports the populations of neighbors, by type, along the population boundary of a particular cell type.
ProgressReporterProgressReporter (Output)LEGACY: ProgressReporter provides verbose output concerning Nanoverse's state and the progress of the simulation. This information should be gradually replaced by slf4j logging with several levels of verboseness.
RandomSeedWriterRandomSeedWriter (Output)Produces a one-line text file for each instance, with the file containing the long integer used to seed the random number generator for the simulation instance.
RunningTimeWriterRunningTimeWriter (Output)Produces a tab-separated text file reporting the simulation and wall-clock running time since the last time the file was updated. Used to track performance.
SurfaceCensusWriterSurfaceCensusWriter (Output)null
TimeWriterTimeWriter (Output)Creates a binary file capturing the number of simulation state updates and the corresponding simulation time. Used in creating visualizations.
VisualizationSerializerVisualizationSerializer (Output)Generates the specified visualization for each instance of the simulation.