<div dir="ltr">Hi,<br><br><div class="gmail_quote"><div dir="ltr">On Thu, Jan 4, 2018 at 10:36 AM Jernej Zidar <<a href="mailto:jernej.zidar@gmail.com">jernej.zidar@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>The "-deffnm" option is very handy because the user doesn't have to specify every single output file (energy, trajectory, log, checkpoint).</div></div></blockquote><div><br></div><div>But what's the requirement for renaming them? The default names are fine - name collisions only arise when someone tries to do their entire (sub)project in the same directory, which IMO is an anti-pattern.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>This option should be kept if it is not too much trouble.</div></div></blockquote><div><br></div><div>The trouble is not the simple case, where it works fine. The trouble is the forest of files that get written by all the modules. There's a lot of infrastructure (and test cases) needed so that all combinations of e.g. mdrun -deffnm -multi -px -append work reliably, now, and under maintenance.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Personally, I'd like to see this option applied to other tools as well (trjconv for example).</div></div></blockquote><div><br></div><div>What's an example use case, please?</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>One suggestion: Would it be possible to have all the tools that analyze trajectories aware of the "-tu" switch ? It's way more convenient to specify the time in ns, ms, ... than in number of steps. </div></div></blockquote><div><br></div><div>Maybe, but perhaps you are referring to -b and -t (which take input in ps, not steps). Again, there's a lot of infrastructure and testing needed to make that work (and potentially confusing if any other time-related option is not also similarly customizable). We've historically done a poor job of that, and now have about as much debt as assets... I don't see enough value in </div><div><br></div><div>gmx tool -tu ns -b 10 -e 20</div><div><br></div><div>vs</div><div><br></div><div>gmx tool -b 10000 -e 20000</div><div><br></div><div>for someone to want to put their time into it.</div><div><br></div><div>Mark</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><br></div><div>Comments?</div><div> </div><div>Cheers,</div><div>Jernej Zidar</div></div><div dir="ltr"><div><br><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 4, 2018 at 5:15 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div>We should also be aware that -deffnm is brittle in the same way that -multi is, because our filename-handling machinery doesn't centralize changing the prefix/suffix needed to support -deffnm or -multi. So I think we should plan to announce -deffnm as deprecated in the 2019 release (and remove after that). If we think that's useful enough to want to keep, we need people to put up their hands for the work to make all the mdrun modules work with it.<br></div><div><br></div><div>Thanks,</div><div><br></div><div>Mark</div></div>
<br></blockquote></div></div></div></div><div dir="ltr"><div></div></div>
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