The tomorun executable has several features and has a relatively rigid structure. If it doesn't quite suit your needs, for example, if you have to integrate over a different state space or using another parameterization, then you are probably better off combining the correct C++ classes into a new, special-purpose C++ program (instead of attempting to modify tomorun to include your use case).

A very minimal version of a "tomorun-like" program is provided in the test suite as "test/minimal_tomorun.cxx".

A couple other examples in the same vein are provided, "test/minimal_tomorun_controlled.cxx" and "test/minimal_single_random_walk.cxx".

You may want to copy one of those examples into a new source file, change the way you specify your inputs (use the Tomographer::MAT classes to read inputs from a matlab file, for example), and generally speaking adjust any other aspect of the program you may want.

The code in "test/minimal_tomorun.cxx" should be commented and understandable. The basic logic is to use the Tomographer::MHRWTasks::ValueHistogramTools classes, in combination with Tomographer::DenseDM::TSpace::LLHMHWalker, to run random walks over quantum states in T-space (see T Parameterization) and collect statistics about a figure of merit. If you have any questions, don't hesitate to ask me.