eljost/pysisyphus: Constraints, new internal coordinates, OpenBabel forcefields, MD improvments

Addition Support for constraints with coord_type: redund, see the documentation Several new (internal, more or less...) coordinates CartesianX, CartesianY, CartesianZ TranslationX, TranslationY, TranslationZ and beginnings of rotational coordinates as in geomeTRIC (see 10.1063/1.4952956 and geomeTRIC) New method to obtain TS-guess based on 10.1002/jcc.23910 that makes use of the new constraints support. See tests/test_birkholz_interpolation for an unit test. xtb-python calculator (PyXTB) OpenBabel force field calculator, using the python interface Ability to specify different isotope masses, e.g., to constrain atoms in IRC runs (see examples/complex/08_hcn_deuterium_tsopt_irc) Many improvements for the internal (still experimental) MD module Very experimental metadynamics support Colvar (CV) gradients from automatic differentiation or explicit implementation Added Bond, Bend and Dihedral CVs (periodicity of dihedrals is not yet implemented) Plotting of free energy curve/surface for 1 and 2 CVs using pysisplot --gau [gau1] [gau2] MD can now be started from YAML input Plotting with pysisplot --md (total energy, conserved quantity, temperature, including running average) Fixed CSVR thermostat Added Berendsen thermostat Dumping to HDF5 Added wrapper script to validate pysisyphus MD runs with physical-validation (see 10.1371/journal.pone.0202764) Internal, small (solvent) molecule DB, preoptimized at different levels of theory, that can also be accessed from the Packmol wrapper pysispack Easy access and usage of benchmark/test sets (Baker, Baker-TS, S22, Birkholz, ...) via benchmarks-subpackage Added test set for COS calculations, intended for GFN2-XTB optimizations Parser for [Geometries]-section in .molden-files rx_mode argument for TSHessianOptimizers. Allows for easy specification of complicated approximate eigenvectors, used for selecting an initial eigenvector for uphill following. rot_disable_pos_curv and trans_force_f_perp arguments for the Dimer calculator. The first one fixes the initial Dimer orientation until the curvature becomes negative. The latter argument controls whether always perpendicular and parallel force components are returned. I-PI-Server calculator that supports the I-PI socket protocol. The present implementation works, e.g., with DFTB+ as client. See examples/opt/10_h2o_xtb_ipi_server for an example. Bugfixes PrimType could not be specified in YAML input when additional primitive internals were requested Velocity is now properly rescaled after removal of v_com Dropped assert that prevented runs with multiple geoms Wrong final energy for Baker-TS case 15 Miscellaneous Printing of additional platform information PySCF verbosity can no be controlled with the verbosity argument First PR from outside of our group, thanks to @bapride11, who improved the Dimer calculator (added rotation_remove_trans) Optimization thresholds are now also plotted in pysisplot --opt Simplified implementation of the using()-decorator that declares test dependencies LinearBends/LinearAngles aren't propagated to the TS guess in run_tsopt_from_cos, as this is usually a bad idea. Now only the bonding skeleton is propagated to the TS guess