Making Sense of MesoRD Output

A typical simulation will create several files. Note that the format of these output files is far from optimal and subject to change in future versions.


This file contains whitespace-separated Cartesian x-, y- z-coordinates and the compartment name, in that order, of every sub volume in the geometry. The coordinates of each sub volume are printed on a separate line. The order in which the sub volumes appear is the same order in which MesoRD has stored them. Note that the file contains no information about how a subvolume is connected to other sub volumes. The compartment belonging is printed along with the coordinates. The unit for the coordinates is number of subvolumes.


Non-Sparse output: This file contains whitespace-separated number of molecules of species X for every sub volume and for each checkpoint. The sub volumes are listed in the order in which MesoRD has stored them. The contents at each checkpoint are printed on a separate line.

Sparse output: If the sparse format has been chosen the files instead gives data only for non-zero subvolumes. In this case the number of the subvolume is followed by the number of molecules in that subvolume, which is followed by the number of the next non-zero subvolume etc. The numbers of the subvolumes corresponds to the line numbers in the geometry file (where the first line is subvolume 0).

In addition, if there does not exist any molecules in any of the subvolumes at a certain time a -1 will be written at the corresponding line in species_X.txt (MesoRD versions 0.3 and later). In earlier versions of MesoRD a blank line was written.


This file contains the simulation time at which each checkpoint was written. Every checkpoint is printed on a separate line.


This file is only created at Windows systems (optionally). On other systems this information is sent to standard output. It contains parsing, geometry building, reaction folding information etc. and also error messages.

Note: If you want to trust the compartment state checkpointing will need to define speciesID:s for all species in every compartment.