Changing the layout of input generators

seal · August 25, 2022, 4:57am

Hello,

Is it possible to combine Charge and Multiplicity into a single row, just as for Theory we have two dropdowns?

Is the code for this window in avogadrolibs/avogadro/molequeue or is it somewhere else?

All the best.

ghutchis · August 25, 2022, 5:56pm

It’s definitely possible… I’m just not 100% sure on what the look would be, which is why I haven’t done it yet. (And truth be told, I’m not sure on whether it’s better to have “+1” and “-1” for charge and “singlet” etc. words for the multiplicities…)

You’d probably want something like:

Charge: 0 Multiplicity: 1

with both labels on one line. It’d require a bit of tweaking. The code is here:

github.com

OpenChemistry/avogadrolibs/blob/2e32152187060eb46495a8462c955e405366f497/avogadro/qtgui/jsonwidget.cpp#L190


      
          // Number of cores next:
          if (userOptions.contains("Processor Cores"))
            addOptionRow("Processor Cores", tr("Processor Cores"), userOptions.take("Processor Cores"));
          
          
// Calculation Type next:
          if (userOptions.contains("Calculation Type"))
            addOptionRow("Calculation Type", tr("Calculation Type"),
                         userOptions.take("Calculation Type"));
          
          
// Theory/basis next. Combine into one row if both present.
          combinedOptionRow("Theory", "Basis", tr("Theory"), tr("Basis"),
                            userOptions);
          
          
// Other special cases: Charge / Multiplicity
          if (userOptions.contains("Charge"))
            addOptionRow("Charge", tr("Charge"), userOptions.take("Charge"));
          
          
if (userOptions.contains("Multiplicity"))
            addOptionRow("Multiplicity", tr("Multiplicity"), userOptions.take("Multiplicity"));
          
          
// Add remaining keys at bottom.

ghutchis · August 25, 2022, 8:48pm

Okay, it looks something like this:

Which reminds me that I need to update the Python scripts to better defaults. (Oh, if we can move Gaussian users to ωB97XD or B97-3c …)

github.com/OpenChemistry/avogadrolibs

Put charge / spin in one line with two labels

OpenChemistry:master ← ghutchis:charge-spin-line

opened 08:46PM - 25 Aug 22 UTC

ghutchis

+29 -20

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seal · August 26, 2022, 2:07pm

Looks nice! It’s worth considering this change because for generators with many options like ORCA, you don’t really see a lot of the input file

I, for example, write the keywords on my own and am only interest to copy the geometry quickly, and so for me 80% of the screen is not useful.

Which actually makes me wonder: maybe there should be an option to just print XYZ and nothing else?

ghutchis · August 26, 2022, 2:37pm

A few of the scripts (Orca in particular) need some re-organization into tabs.

You could certainly write an “input generator” with no options: GitHub - OpenChemistry/avogenerators: Python input file generators for Avogadro 2

You can also take a look at the coordinate editor (Build => Atomic Coordinate Editor):

Since you mention Orca, you should know that you can use the *xyzfile [charge] [spin] option to simply read from an XYZ file. We do this a lot, since we can have standardized keywords for jobs and just read the relevant geometries.

seal · August 26, 2022, 6:40pm

I didn’t notice this before, thank you! Is it possible to assign a keyboard hotkey to that window? Just as option-command-o does optimization, maybe there could be option-command-e for coordinate editor?

I’m aware of that, thank you. I use it whenever I start calculations on top of previous ones. The only issue is that exporting XYZ is much slower (more clicks, need to navigate to the required path, if you need geom on a server then you also need to do scp) than copying it from input widget (or coordinate editor) and pasting wherever you need it.