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Regression tests broken

BeamLine-1, BeamLine-2 and PROSCAN-1 regression tests are broken due to an increase of execution time. The simulations spend more time than the maximum time specified in the mpirun command. Removing timeout option, the regression tests are passed successfully.

In addition, the reference output files for the BeamLine-1 and BeamLine-2 tests previously ended with an error, so they need to be updated.