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Result Files
During the course of a simulation, iDynoMiCS will save output files describing the current solute fields and agent states. These output files will be written at the interval specified by the outputPeriod parameter in the simulator mark-up.
After each output period, six different XML files are written:
- agent_State(nFile).xml
- agent_Sum(nFile).xml
- agent_StateDeath(nFile).xml
- agent_SumDeath(nFile).xml
- env_State(nFile).xml
- env_Sum(nFile).xml
In each file name, nFile represents the iteration number at which the file was written. The agent_State and agent_Sum files describe the state of the agents in the system; the agent_State file describes each agent in detail, while the agent_Sum file summarizes the agents on the species level. The Death version of these files lists all agents that have been removed from the system at the given iteration and includes the reason for the agent’s death: too small, detached, over board (i.e. killed by the boundary bulk for trespassing) or washed away by dilution in the chemostat case. Similarly, the env_State and env_Sum files describe, respectively, the overall state of the solute fields and a more summarized version.
After being written, each result file is also copied to a zip archive kept for each type, with the most recently written state always being accessible in the lastIter directory. Note that these files can take up several megabytes each, so be careful when choosing the outputPeriod parameter to avoid taking up too much disk space.
In addition to the numerical description, a .pov file describing a picture of the agents in the biofilm is also written. This file can be processed using the POV-Ray software.
We now describe the output files in a little more detail over the next few pages. If you are reading the PDF version of this tutorial on screen, clicking on the section will take you to the relevant page on the iDynoMiCS wiki on github. The information in this document is however the same as that found on the wiki.