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More often than not, the time spent on collecting the information necessary to properly define an adequate model of the (part of the) process you are interested in is much greater than the time spent by a simulator program in finding a solution.
Physical topologies are the abstract representation of the containment of the process in the physical sense. They visualise the principle dynamic contents of the process model and therefore the construction of a physical topology is the most fundamental part of the modelling process.
The idea of the construction of the species topology is to facilitate the definition and identification of species and reactions occurring in various parts of the processing plant. The species topology defines which species are present in which part of the process.
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