Viperleed

See betatest repository for executable.

- Switched default separator in CSV input/output files back to comma (from semicolon). Semicolons will still be accepted in input files.
- Fixes a major bug in applying unit cell scaling during full-dynamic optimization
- Fixes some issues with saving fortran-compile.log files for diagnosis
- Reduced angle tolerance for unit cell type detection and increased code consistency. This prevents some incorrect assignment of rhombic cells as hexagonal. However, this should not have caused any problems aside from incorrect cell types reported in the log files.
- Fixed an issue that made it impossible to use the control.chem file as a starting configuration for a new search, because old output files were cleared from the working directory at the beginning of tleedm execution. Output files that can also serve as input (control.chem, refcalc-fd.out and superpos-spec.out) are now kept until needed, but still deleted at the start of the respective segments to avoid mistaking them for new output.
- DISPLACEMENTS direction statements are now more tolerant to whitespace, e.g. '[ 1 -1]' or '[ 1 -1 ]' are accepted in place of '[1 -1]'.
- TensErLEED: fixed an issue that made versions >= 1.71 ignore V0_REAL input
- TensErLEED: Added output of complex amplitudes in reference calculation as 'amp.out'; ViPErLEED processes these to produce new files 'Complex_amplitudes_real.csv' and 'Complex_amplitudes_imag.csv'.

**Features:**
- Added segment "full-dynamic optimization", which iterates "reference calculations" (without Tensor output) to optimize parameters not accessible by Tensor LEED search (i.e. beam incidence angles, V0i, unit cell size). Behaviour is controlled by new parameter OPTIMIZE. See documentation for details.
- THEOBEAMS.csv are now also output as plots in THEOBEAMS.pdf (raw data without smoothing or interpolation).
- Slightly modified storage of original input files and fortran compile logs in both tleedm and bookkeeper. This should reduce the potential for user behaviour affecting the "history" folder. For example, "original input" from tleedm execution is now stored in a dedicated subfolder in SUPP such that even if input files are modified before the bookkeeper is run, it is still possible to reconstruct the input files used for generating a specific output.

See betatest repository for executable. Tag v0.7.0-b includes some fixes made before publication on betatest repository, corresponds to 0.7.0 there.

**Features:**
- Added parameter SYMMETRY_BULK, which allows manually setting a bulk symmetry other than the automatically detected one. See documentation for details.
- included preliminary support of new EEASiSSS version. Currently accessible via "PHASESHIFTS_CALC_OLD = False" parameter, which will be removed once we are convinced that the new version is stable and should always be used.

**Debugging:**
- fixed a bug that prevented mpifort compiler from being recognized
- fixed an issue that sometimes crashed the search if SD.TL was written at an inconvenient time (mainly on macOS)
- fixed an issue with cleanly terminating the search through user intervention (sometimes leaves zombie processes)
- fixed an issue when reading refcalc output: TensErLEED sometimes produces unusual formatting (seen only on macOS)

See viperleed-betatest repository for executable.

**Features:**
- added an optional parameter BULK_LIKE_BELOW that can be used to automatically detect N_BULK_LAYERS, LAYER_CUTS and BULK_REPEAT from the POSCAR file. See documentation for details.
- added a parameter AVERAGE_BEAMS that allows switching off the averaging of equivalent beams, or to average according to a different beam incidence than given by BEAM_INCIDENCE. **Note:** Correct averaging for off-perpendicular beam incidence is currently not supported, but will be fixed in an upcoming release!
- RUN parameter now allows string aliases for the different segments, e.g. "ref" for reference calculation, "init" for initialization, etc. See documentation for details.
- added a parameter in TensErLEED v1.71 search input search.steu that allows switching off the hash table storage of past configurations. This may slightly affect performance for long-running searches with few parameters, but improves performance in most cases, and saves some memory. However, PARABOLA_FIT cannot be used since the necessary data output will be missing. tleedm will switch storage off if PARABOLA_FIT is off.

**Minor changes:**
- turned PARABOLA_FIT off by default (as it affected performance and was not very reliable)
- made POSCAR output preserve the scaling factor of the input POSCAR, instead of always setting scaling to 1.
- Input files PARAMETERS, DISPLACEMENTS and VIBROCC now accept characters "%" and "" to indicate the beginning of a comment, in addition to "!"
- changed default of ATTENTUATION_EPS to 0.001
- checked the non-parallelized search modules of TensErLEED, and made ViPErLEED use those for single-node jobs if no fortran MPI compiler is present. Therefore, it is now possible to run ViPErLEED for simple systems without installing an MPI compiler, although this is not recommended for serious operation.

**Debugging:**
- fixed a bug in ViPErLEED that led to variations of concentrations being ignored in DISPLACEMENTS if the initial site occupation was mixed
- fixed a bug that led to incorrect comparison of experimental and theoretical beams in R-factor calculation if experimental beams were dropped (due to missing theoretical counterpart)
- fixed several issues with TensErLEED v1.71, and with ViPErLEED reading TensErLEED results with modified formatting.
- fixed an issue in TensErLEED superpos that would add an additional header line to the output spec.out if more than 200 Delta files were used

- Introduces flexible input and output formatting to be compatible with TensErLEED v1.71. This also entirely removes the muftin.f file in the reference calculation. Backwards compatibility to older TensErLEED versions is preserved, and older versions can be selected by the already established TL_VERSION parameter. Phaseshifts still use the "old" EEASiSSS code by John Rundgren (and expect the corresponding file format), an update to allow usage of newer versions and phaseshift file formats will follow. Note that some changes in TensErLEED v1.61 by fkraushofer are not yet merged into TensErLEED v1.71, making some ViPErLEED features (especially the multidimensional parabola fit during search) temporarily unavailable.
- Fixed a bug introduced in v0.5.6 that caused concentration variations to be ignored
- Fixed a bug that caused tleedm to crash when compiling the search with the mpifort (instead of the mpiifort) compiler
- Fixed a bug in symmetry detection affecting a special case of hexagonal unit cells with cm symmetry, which occured when the mirror plane was parallel or perpendicular to one of the unit vectors, rather than parallel to one of the unit cell diagonals