Aqme

- Fixed bug for using constraints with large molecules in CREST (related to long atom lists
in the .xcontrol.sample file that weren't compatible with subprocess.run())
- Fixed bug when using squareplanar templates with ligands that bond with the metal centers
with the same type of atom (but they are different ligands)
- Added the 'Ir_squareplanar' geometry rule
- Better print for command lines (more reproducible commands)
- QDESCP adds an initial xTB optimization before the single-points (before, the descriptors
were obtained from RDKit geometries, and they were pretty bad for metal complexes)
- The aqme.py file now takes all the arguments from command lines with vars(args)
without specifying the argument names explicitly in the code
- Added the chk_path option to add PATH into chk lines
- Added the xtb_opt option to optionally disable the initial xTB geometry optimization in QDESCP
- Fixed a bug when an xTB calc failed, the whole QDESCP workflow stopped (now the specific
conformer just gets ignored)
- Fixed bug when GB or MB were not part of the mem argument in QPREP-ORCA
- Added the qdescp_opt option for adjusting the convergence criteria of xTB in QDESCP
- DBSTEP calcs are deactivated by default in QDESCP (activate them with --dbstep_calc)

- A second ConstrainedEmbed() function with a core with no Hs was added to avoid
RDKit embedding issues that show up in tricky cases
- Fixed the --charge and --mult options when using xyz/sdf/pdf/gjf/com files as inputs in
CSEARCH (xyz fixed in QPREP as well)
- Options low_check and e_threshold_qprep were added to QPREP (create inputs only for n
conformers of below a certain energy threshold)
- Option nodup_check was added to QCORR (turns off the duplicate filter)
- DBSTEP buried volume added in QDESCP with the qdescp_atom option
- Atomic properties of a single atom type were added in QDESCP with the qdescp_atom option
- Creation of databases for AQME-ROBERT workflows with the --robert option (True by default)

- QCORR is compatible with directories that contain a "." symbol
- QCORR is compatible with ORCA calcs (it doesn't detect spin contamination yet)
- QCORR includes hessian calculations for calcs with extra imaginary frequencies by default
(new option to control this: im_freq_input)
- QCORR tries to fix SCF convergence issues in ORCA by adding the SlowConv keyword
- qm_end option is added after the genecp section in QPREP
- Fixed a bug when using the destination option in CMIN-xTB

- The files and input options are compatible with partial PATHs, full PATHs, and direct names
from command lines and Jupyter Notebooks
- The SUMM option was fixed in CSEARCH
- The files and input options now tolerate PATHs that contain directories with "." characters

- Suffix/prefix options work in CSEARCH, CMIN and QPREP
- Automatic recognition of metals with the auto_metal_atom option
- In QPREP, if qm_input starts with "p ", the Gaussian inputs starts with "p"
- CSEARCH-CREST updates the CREST outfile as the program calculates (not at the end only)

- When using a CSV as input, the user can specify charge and mult for each species by
using the charge/mult columns
- QCORR now detects duplicates including the successful calculations from previous runs
- Fixed an error in full_check from QCORR when using genecp
- Admits lists in command lines specified as ["X"], "[X]" and '["X"]'