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The third clause of the 3-clause BSD license says:

  1. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

I want to publish a software tool developed by me that I use for my research. From this question on Academia.SE, I know that licenses that try to enforce citations of the software when used by other researchers have disadvantages, and it is better for me to "ask nicely".

But let us assume another researcher runs simulations that partially use my code and publishes the results in a journal. Maybe they also publish the full code (which includes my tool), or maybe not: I do not want to enforce this and I am interested in the implications of both cases. Does the third clause prevent them from citing me in their journal publication unless they ask me for permission first? This is not something I want.

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No, the third clause of the BSD license does not prevent an academic citation of your work. What it prevents is statements along the lines of

Because we have made use of tool X by @wimi, they support the outcome of our research into <controversial topic>

or

These results were made possible by six years of effort by (Author A), (Author B), (Collaborator X) and @wimi who were funded by (Grant Y) and (Grant Z)
from comment by @Ben Voigt

or

Our program is the best because, unlike its competitors, it uses the code produced by YY
from comment by @supercat

or more subtle forms of endorsement/promotion.

In essence, it means that people using your tool or building upon your tool may not state/imply that you have particular thoughts about those further developments without getting a separate explicit permission to publish your thoughts.
It does not forbid a neutral mention that your tool was used.

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    I think the clause would also distinguish between a statement "This code uses the XX library produced by YY" versus "Our program is the best because, unlike its competitors, it uses the code produced by YY", allowing the former but not the latter.
    – supercat
    Dec 17, 2019 at 22:14
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    I think a more realistic example would be something like "These results were made possible by six years of effort by (Author A), (Author B), (Collaborator X) and @wimi who were funded by (Grant Y) and (Grant Z)" which falsely implies that wimi was working toward the same overall goal.
    – Ben Voigt
    Dec 17, 2019 at 23:48

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