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"Error in tree structure" is a very unusual error message that is generated by the TMSL model compiler in case of a malformed equation LHS. As such it has nothing to do with preprocessor defines, at least not directly.
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This issue should be solved as of WEST2017, and possibly also in WEST2016 SP2.
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You are using the 64-bit version of WEST without having a separate C compiler installed. If you don't want to install a C compiler separately, use the 32-bit version of WEST. For more information, please read through the attached document.
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No. Calculator variables can be regarded as some form of post-processing. They are not part of the executable model and can hence not be used as input to one or the other block.
For what you want to do you will either have to create a custom block, or add top-level equations. The first should work in all versions of WEST, the latter requires WEST 2017 or higher.
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Actually, each category (primary and other) should have a corresponding loop breaker model. On top of that (as Youri correctly points out) there should also be a loop breaker model for scalars (cf. Data / Control).
Note that when activating the InsertLoopBreakers option, the software will only be able to insert one particular loop breaker model automatically (the one specified through the LoopBreaker property), so there are several classes of algebraic loop situations that can only be solved by placing the appropriate loop breaker(s) manually.
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If you just want the "final" integral (i.e. at the end of the simulation, over the entire horizon) of a calculator variable, you can add that calculator variable as a variable to the objective evaluation and tick the integral time series criterion. If you don't want this integral to be taken into account for the overall objective value computation, you can set the weight of the integral criterion to 0 (or set the weight of the variable to 0 if the integral is the only criterion that is active).
If you want the integral to be computed at every time point, you cannot do with calculator variables. Calculator variables are in fact the old (pre-2017), limited approach to defining additional top-level computations. The new top-level items window (that Enrico is referring to) supersedes the old calculator variables and also adds extra possibilities such as aggregation (e.g. integral computation) and much more. Actually, the top-level items approach even allows for computing the integral in 2 ways: through a differential equation and through the MSLUBuffer functionality. The first is the simplest, but the latter is more versatile since it allows for using a moving window for the integral computation (should this be necessary).
See the attached screenshot.
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Selecting one of the "properties" items in a plot's context menu will display these properties in the "Properties" Window. If you can't see this window, you may have to go to View / System / Properties in the main menu (or alternatively press Ctrl-W, P). See also the User Guide.
For displaying a unit on for instance the Y axis, go to the "Axes properties" and then to Left / Title, and set Text to a string that includes the unit.
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For SRT, you may want to have a look at the document "WEST: How to compute SRT and HRT?" in http://userarea.west.mikepoweredbydhi.com/FAQ/
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Temp_Ref (reference temperature of activated sludge) is a parameter (default value: 20°C) that can be set by the user and normally doesn't change. See for instance the TwoASU_PE tutorial. I don't know why it would unintendedly change in your case.
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You can find information in Section 4.2.1 of the User Guide (WEST 2016), and in Section 8.3.3 of the attached PhD dissertation.