MesoRD Code

The molecule tracking module now provides a log file with the following information:

- length of a voxel (-q option)
- timestep between position outputs in trajectory.txt files (-w option)
- list of pairs of speciesnames and diffusion constants, in the same length & time units as used for the voxels and timesteps

More changes for allowing compilation on Unix systems via CMake.

Change of several files, especially the CMakeLists.txt files to allow compilation on Unix systems via CMake.

Creation of the molecule tracking version of tutorials.xml, called tutorial_molecule_tracking.xml

Tested MesoRD on tutorial_molecule_tracking.xml and everything seemed to work.

Modified the XML files to have MesoRD:species instead of MesoRD:species_diffusion in the species field.

Added more flags HAVE_MOLECULE_TRACKING where there was molecule tracking specific code.

Several small optimizations regarding data access and more appropriate data types. Overall gain might be around 1% but that should be tested more in depth.

In the XML file, the field "MesoRD:species_diffusion" is now "MesoRD:species".

It is now possible to have mature molecules from the start. To do so, one must add a field to the species definition in the XML file:

<MesoRD:mature_initial MesoRD:initialAmount="50"
                       MesoRD:units="percent"/>

in MesoRD:species. The amount can be in "item" or in "percent" of the initial amount of the species.

Molecule tracking successfully runs with two compartments.

When a mature molecule moves to another compartment and the diffusion constant is different in the new compartment, then this event is added to reactions.txt

Updated some of the test files.

Ran the tests, everything ran successfully.

Fixed a bug where dead molecules were still printed in the first line of trajectories.txt

The id of the first molecule created is now 1 instead of 0 in order to facilitate the processing of output files by Matlab.

The name of the fluorescent maturation reaction is now "maturation" instead of "fluorescence".