Moved stop(kill) command to runner

Samo Penic

2016-05-24 f066597dcbb2980d503725defe18e62770bfa9cb

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Original written by Dan Kroll in FORTRAN. Code was then largely adapted and commented by Miha Fosnaric-Fosni. Rewritten into C by Samo Penic-Peni, with help of Miha's extensive explanations.