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Juliette,
this is not directly possible, but you can open the dac file while FEFLOW is running to check what the last time step calculated was.
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I would recommend that you go through the demonstration exercise described in the booklet of the FEFLOW DVD. I think this will answer most of your questions.
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In this case your boundary conditions are probably all on the active slice. Then all options will give you the same result.
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If the channel bed elevation is not constant, but spatially distributed, you can also use the 'data' option of the join tool (instead of 'const') to do an interpolation for the nodes within a polygon only.
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No, the binary formats are not documented. For manipulating the files outside FEFLOW, you have to use the ASCII formats.
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1. Yes, they are.
2. Air is considered as non-existing for heat storage and conduction, i.e., it does neither store nor conduct heat.
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FEFLOW 5.3 can plot scatter diagrams for a comparison of calculated and observed head. Please see the FEFLOW online help system for details (e.g., in the "What's new" section).
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In this case, I'd simply set a fixed temperature to the injection node (1st kind boundary condition for heat transport).
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A well for heat transport is a point source for heat. It does not have to be an actual well. Please note that you have to use the divergence form of the transport equation when using point sources for heat ('Well' type conditions).