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Improvements to Report files tab #15
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Thanks for the feedback! To help keep track of these I'm going to be editing this reply as I address them.
The index is the same as that in the original input file (the ASE index is just that minus one).
I think the MV2-generated labels (generated in cases where the loaded file doesn't have CIF-style labels) are useful to compare what the user sees in the GUI (they can show these labels in the Select and Display sidebar) with what's in the output file. Would you recommend changing the column header to 'MV2-generated label' or similar in such cases? |
One additional question I have is about the multiplicity. At the moment, the files output is always determined by the current selection of atoms. When calculating the multiplicity, is it safe to assume that that user wants the multiplicity within the current selection, or should we instead give the 'global' multiplicity (i.e. how many times each label appears in the loaded file, regardless of the current selection)? At the moment I assume the user wants the multiplicity within the selection and have added a tooltip explaining this. If no atoms are selected then all atoms are exported and the 'global' multiplicity is given. |
Apologies for the confusion. The index, as it currently stands, is simply a counter following the order of the atoms in the .magres file. i.e. index 1 is the first atom listed in the magres file and atom 47 is the 47th etc. It's more tricky in the case of CIF files having more than P1 symmetry -- then the indices are determined by the application of the symmetry operations (when the file is loaded, the symmetry is essentially reduced to P1). This is only potentially problematic for outputting dipolar couplings of such files. I'll switch to using "number in species label". |
Hi @jkshenton . Some additional points following more usage. I don't think the "File type" thing has been changed (I was checking on your development version)? I would also change the menu entries to "MS", "EFG" etc. i.e. drop the unnecessary "table". Merge equivalent labels should be greyed out / replaced with a message about no merging being possible if there are no labels. [I would have this a key flag associated with a structure (it is not going to change)]. Otherwise you have a tick item that does nothing. You should be able to export as shifts - it is odd being able to plot shifts but not export them. Either this could be another menu option (probably more elegant), where it is an error to try to export shifts for elements with undefined references, or it could be an additional column with blank entries where no reference has been set. CSV is happy with blank entries, but it would create import complications e.g. numpy will not like heterogeneous data. |
- consolidated options in sidebar - option to merge by CIF labels if present - csv or fixed width option - precision control Partially addressed issue: CCP-NC#15
- labels and indices now match the .magres file - Indices correspond to the "number in species label" from the .magres Partially addresses issue: CCP-NC#15
Some quick critiques on the Report files tab, just looking at shielding for now:
I wouldn't put "Select and display" on its own line - bold does the highlighting.
"File type" -> "Output" [you're not changing the file type]
Below I would have "Options:" and move "Include" to "Euler angles"
"Merge equivalent labels" appears 3 times. I would have one tick box with a tool tip. It's not obvious what would happen if the file didn't have crystallographic labels?
If merging, there should be a column for “Multiplicity”. Particularly for inorganic systems the multiplicity will be site dependent.
Would "export as shifts" be available if referencing were set?
In the file itself:
The output seems to be based on fixed columns, which is horrible. I think tab separated is a sensible default, since it's vaguely readable. You could have comma separated as an option (I don't think , is likely in output).
The comment lines must be preceded by a comment character. # is a sensible choice (default for numpy).
A more informative comment would be "MS table generated by MagresView 2 from " (assuming shielding output). Including any parameters e.g. referencing used gives full reproducibility.
Element -> "Isotope". Although if you are outputting isotope-independent properties, I think it is smarter to output element (i.e. Z).
I don't understand the index column. Is this based on the ASE index? This will make no sense to the user. Any index should reflect the original input.
Similarly I would only use "Label" if these are user-labels.
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