Merge OpenMP branch to master

[macrocosme]

This pull request includes addition of the option to utilise OpenMP (or not) to parallelize a number of compute intensive code sections.

[ymaan4]

In a test run using a common input data file and same command line parameters, the output data files from the current master and the dev_omp_merged branch seem to not match with each other. The comparison was done using the 'diff' command. The variable indicating the number of threads was not used, so the default number of threads were used in this test run.

[macrocosme]

I'll have a look soon then. It must be that something got mixed up during merge.

[macrocosme]

The issue has been fixed. The problem was related to the introduction of the variable thread_num in cleanit() that was not included as private for the omp parallel for blocks. I tested running after compiling with openmp for 16 threads and 1 thread, as well as without openmp, and the outputs were the same in all cases.