Viperleed

Patches some bugs in tleedm and bookkeeper.

- *bookkeeper*: When bookkeeper was called with the -c / --cont option, it would sometimes grab the POSCAR_OUT_parabola instead of the normal POSCAR_OUT. Since the parabola fit is not very reliable at the moment, this may yield much worse continuation structures.
- *tleedm*: Fixed a misnamed variable in search that would cause tleedm to crash if no SD.TL file was produced for more than 15 minutes.
- *tleedm*: Fixed a bug in initSites that would stop tleedm if an element name occured both as a POSCAR element and in ELEMENT_MIX for a site with a different POSCAR element (e.g. a mixed Au/Cs site called Int in a POSCAR that also contains pure Au sites).
- *tleedm*: Fixed an issue with assigning occupation variations, which didn't allow any of the elements to be kept at constant concentration while other vary (because the range would technically have only one "step"). One-step assignments are now allowed, and will be extended to the number of steps of other elements under variation.

- *tleedm / bookkeeper*: Renamed the AUX folder to SUPP (for "supplementary" / "supporting"). This is for compatibility with Windows, since Windows does not allow a directory or file to be named AUX.
- *tleedm*: Disabled EnvironmentErrors that would normally stop execution when running on Windows
- *tleedm*: Fixed minor bug in automatic detection of bulk repeat vector. Functionally, everything worked fine, but the correct bulk repeat vector was not correctly output in the POSCAR_bulk file.
- *tleedm*: Minor debugging and improvements in formatting of the error calculation output
- *gui*: Fix more bugs preventing saving to file; connect export button.

**Feature changes:**
- *tleedm*: Added automatic detection of the bulk repeat vector: As long as the bulk is defined correctly by N_BULK_LAYERS (and LAYER_CUTS, if necessary), and there is a sufficiently bulk-like layer directly above the bulk, the bulk repeat vector is now detected automatically (if not defined manually), and written to PARAMETERS during initialization. See documentation on BULK_REPEAT parameter for details.
- *tleedm*: Renamed _BEAMLIST file to BEAMLIST. The BEAMLIST is now treated as an AUX file. This is more consistent with the other input/aux/output files, as the BEAMLIST is always re-generated at initialization, and cannot be supplied by the user directly.
- *tleedm*: Renamed _PHASESHIFTS to PHASESHIFTS. The underscore was originally meant to highlight that the _PHASESHIFTS file may have been generated automatically, and is not a required input file, but this distinction is no longer helpful.
- *gui*: Add pre-release notice via a popup at startup

**Bug fixes:**
- *tleedm*: Resolved a bug that would reset search population to random configurations and then stop. This happened when the search reached "partial convergence" before the SD.TL file had been read, if simultaneously the control.chem file was corrupt or nonexistent.
- *gui*: fix bug that prevented from saving input files
- *gui*: fix bug that swapped bulk and surface cells in the header of exported pattern files

Patches issues in tleedm. For latest GUI version, see release v0.1.0

- Fixes several issues with more complex error calculations. Most problems arose around the case where some parameters are varied, but other parameters are kept constant at an offset from the reference calculation, and therefore their deltas also need to be included in the superpos.
- Fixes minor issues with plotting the error curves.
- When stopping delta calculations with the STOP parameter, subprocesses are now immediately terminated by a kill command, instead of simply terminating the pool (which kept the subprocesses running).

Updates tleedm and bookkeeper. For latest GUI version, see release v0.1.0

<b>Feature changes:</b>
<ul>
<li>Implemented "Error calculation": Calculation of R-factors for one-dimensional parameter variations. Note that fd.out files are now included in the Tensors.zip archives, and are required for error calculations, so old Tensors archives may not be compatible.</li>
<li>Limits of the displacements ranges are now labelled on parameter plots in search-progress.pdf and search-report.pdf</li>
<li>More detail is included the "generations since last change" plot in search-progress.pdf</li>
<li>Improved legend for the "parameter scatter" plot in search-report.pdf</li>
<li>Bookkeeper now automatically adds information from "notes" or "notes.txt" files to history.info automatically</li>
<li>Improved functionality of TENSOR_OUTPUT parameter</li>
<li>Initial tleedm cleanup now removes old AUX and OUT directories and files from previous runs in the work folder</li>
</ul>

<b>Bug fixes:</b>
<ul>
<li>Fixed incorrect symmetry linking through mirror+rotation (occured for p3m1)</li>
<li>Fixed crash when search was called with no parameter variations</li>
<li>Fixed a crash with bad error message if VIBROCC is missing</li>
<li>search-PARAM was missing from AUX files, now added</li>
</ul>