MesoRD Code

The path to config.h file was modified from:

../config.h

to

../../config.h

Now the trackingTimeStep and trackingTimeInit for molecule tracking are options that can be set in the command line with:

-w : set the tracking time step, i.e how often you want the trajectories to be updated (seconds)

-x: set the tracking initial time, i.e when should the outputs (reactions.txt and trajectories.txt) start being updated. (seconds)

The letters are maybe ill-chosen but there are not so many available anymore, so I picked consecutive letters.

The reactions.txt and trajectories.txt are now only updated after the time defined by tracking_time_init (in seconds) to only print out the reactions and the trajectories once the system is stable.

trajectories.txt does not print out a molecule once it disappeared (previously it printed the last position of the known molecule, ie where it died).

Fixed a bug reagrding the number of reactants when one species turns into another (A->B).

Fixed compilation issues on Linux. Inlcude paths and configure script changes

bootstrap and Makefile (root folder) have Unix style end of line.

Fixed a bug regarding the number of reactants in a subvolume (incremented for the molecule tracker after a destruction event).

First working version of the molecule tracking addition to MesoRD. To activate it, set HAVE_MOLECULE_TRACKING to 1.

Reactions where 2 or more reactants have a fluorophore are not supported.

When a reaction with more than one product happens, then the product which should inherit the fluorophore has to be the first in the list of products in the xml file.

The binary folder should not be in here. My mistake.

Implementation of CMake as a compilation file generator.
Successful compilation on Win 64 machine.
Unsuccessful on Ubuntu 64 server (work in progress).

Implementation of Molecule Tracking functionality.

implementation of CMake as a compilation file generator.
Successful compilation on Win 64 machine.
Unsuccessful on Ubuntu 64 server (work in progress).